An ultrafast memory-efficient short read aligner
C++ Perl Shell C Python Makefile Objective-C
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SeqAn-1.1 trying to bring thread affinitization, various lock types, TBB fully … Mar 20, 2016
doc updated contributors; removed cruft Dec 31, 2016
genomes *** empty log message *** Jan 14, 2009
indexes *** empty log message *** Sep 7, 2010
reads *** empty log message *** Sep 7, 2010
scripts Add DNA perl module Nov 29, 2016
third_party release 1.0.1 Mar 20, 2014
.gitignore adding gitignore Jul 23, 2014
.travis.yml fix CI test failures Dec 20, 2016
AUTHORS Updates for v1.0.0 release Apr 9, 2013
LICENSE Added README and renamed COPYING to LICENSE to be more GitHub-friendly. Dec 21, 2012
MANUAL Update documentation for release 1.2 Dec 20, 2016
MANUAL.markdown Update documentation for release 1.2 Dec 20, 2016
Makefile Modify rules for building packages and running tests Dec 20, 2016
NEWS Update documentation for release 1.2 Dec 20, 2016
README Added README and renamed COPYING to LICENSE to be more GitHub-friendly. Dec 21, 2012
TUTORIAL fixing e coli link and instructions Nov 8, 2016
VERSION Update documentation for release 1.2 Dec 20, 2016
aligner.h fixed several bugs related to --skip, raw input Oct 20, 2016
aligner_0mm.h trying to bring thread affinitization, various lock types, TBB fully … Mar 20, 2016
aligner_1mm.h trying to bring thread affinitization, various lock types, TBB fully … Mar 20, 2016
aligner_23mm.h trying to bring thread affinitization, various lock types, TBB fully … Mar 20, 2016
aligner_metrics.h *** empty log message *** Mar 29, 2009
aligner_seed_mm.h *** empty log message *** Dec 5, 2009
alphabet.cpp Simplified makefile. Made alphabet source file into C++ Dec 15, 2012
alphabet.h Fixed clang warnings Dec 15, 2012
annot.cpp For review; Passing first tier of tests. Jul 16, 2014
annot.h For review; Passing first tier of tests. Jul 16, 2014
assert_helpers.h *** empty log message *** Aug 27, 2010
auto_array.h *** empty log message *** Oct 21, 2009
binary_sa_search.h many changes that fix LFS bugs and make implicit casts explicit Jun 25, 2014
bitpack.h Streamlining and slimming down the contents of the bowtie module in p… Aug 13, 2008
bitset.h trying to bring thread affinitization, various lock types, TBB fully … Mar 20, 2016
blockwise_sa.h For review; Passing first tier of tests. Jul 16, 2014
bowtie Add support compressed input files Jan 11, 2017
bowtie-build revive bowtie-build and bowtie-inspect scripts Nov 4, 2016
bowtie-inspect revive bowtie-build and bowtie-inspect scripts Nov 4, 2016
bowtie_build_main.cpp many changes that fix LFS bugs and make implicit casts explicit Jun 25, 2014
bowtie_inspect.cpp fixing incorrect delete Jan 11, 2016
bowtie_main.cpp many changes that fix LFS bugs and make implicit casts explicit Jun 25, 2014
btypes.h fixing misspelling and some bugs Jul 17, 2014
ccnt_lut.cpp *** empty log message *** Jun 2, 2009
chaincat.cpp *** empty log message *** Sep 8, 2009
color.cpp *** empty log message *** Nov 24, 2009
color.h *** empty log message *** Nov 24, 2009
color_dec.cpp many changes that fix LFS bugs and make implicit casts explicit Jun 25, 2014
color_dec.h *** empty log message *** Nov 24, 2009
cpu_numa_info.cpp getting rid of dependence on libnuma Mar 24, 2016
cpu_numa_info.h getting rid of dependence on libnuma Mar 24, 2016
diff_sample.h many changes that fix LFS bugs and make implicit casts explicit Jun 25, 2014
ebwt.cpp test updates Apr 22, 2014
ebwt.h Added the rewind fix pointer. Jul 18, 2014
ebwt_build.cpp test updates Apr 22, 2014
ebwt_search.cpp Add missing quotation mark Dec 20, 2016
ebwt_search.h trying to bring thread affinitization, various lock types, TBB fully … Mar 20, 2016
ebwt_search_backtrack.h many changes to bring bowtie batch parsing more in line with bowtie2.… Oct 19, 2016
ebwt_search_util.cpp *** empty log message *** Nov 24, 2009
ebwt_search_util.h trying to bring thread affinitization, various lock types, TBB fully … Mar 20, 2016
edit.cpp *** empty log message *** Oct 19, 2009
edit.h *** empty log message *** Oct 19, 2009
endian_swap.h In work. From this point we temporarly break bowtie functionality. Mar 11, 2014
fast_mutex.h Added the tiny thread spinlock and started the tiny thread usage impl… Mar 21, 2013
filebuf.h Merge changes from pull request 25 Nov 29, 2016
formats.h *** empty log message *** Feb 1, 2010
hit.cpp many changes that fix LFS bugs and make implicit casts explicit Jun 25, 2014
hit.h Merge changes from pull request 25 Nov 29, 2016
hit_set.cpp *** empty log message *** Nov 24, 2009
hit_set.h many changes that fix LFS bugs and make implicit casts explicit Jun 25, 2014
log.cpp *** empty log message *** May 8, 2009
log.h trying to bring thread affinitization, various lock types, TBB fully … Mar 20, 2016
mm.h Buffered all file access (originally suggested by James) Jul 18, 2014
multikey_qsort.h many changes that fix LFS bugs and make implicit casts explicit Jun 25, 2014
pat.cpp Enable reading from stdin Jan 18, 2017
pat.h getc_unlocked is an alias for _fgetc_nolock when compiling on Windows Dec 19, 2016
pool.h *** empty log message *** Apr 5, 2010
processor_support.h Dropped the intrinsics dependency and replaced popcnt with plain asm … Jan 14, 2014
qual.cpp *** empty log message *** May 5, 2009
qual.h *** empty log message *** Sep 25, 2009
random_source.h These still needs review. Jun 9, 2014
random_test.cpp *** empty log message *** Dec 11, 2009
range.h These still needs review. Jun 9, 2014
range_cache.h many changes to bring bowtie batch parsing more in line with bowtie2.… Oct 19, 2016
range_chaser.h For review; Passing first tier of tests. Jul 16, 2014
range_source.h many changes to bring bowtie batch parsing more in line with bowtie2.… Oct 19, 2016
ref_aligner.cpp *** empty log message *** Feb 9, 2009
ref_aligner.h many changes that fix LFS bugs and make implicit casts explicit Jun 25, 2014
ref_read.cpp many changes that fix LFS bugs and make implicit casts explicit Jun 25, 2014
ref_read.h fixed mingw failure to compile. Jul 19, 2014
reference.h fixing warning related to binarySearched Apr 9, 2016
refmap.cpp For review; Passing first tier of tests. Jul 16, 2014
refmap.h More work. Code compilable now. Apr 17, 2014
row_chaser.h For review; Passing first tier of tests. Jul 16, 2014
sam.cpp Merge changes from pull request 25 Nov 29, 2016
sam.h More work. Code compilable now. Apr 17, 2014
search_1mm_phase1.c *** empty log message *** Nov 26, 2009
search_1mm_phase2.c *** empty log message *** Nov 26, 2009
search_23mm_phase1.c *** empty log message *** Nov 26, 2009
search_23mm_phase2.c *** empty log message *** Nov 26, 2009
search_23mm_phase3.c Fixing warnings Dec 15, 2012
search_exact.c many changes that fix LFS bugs and make implicit casts explicit Jun 25, 2014
search_globals.h Added mode to output primer base and first color for colorspace reads May 7, 2012
search_seeded_phase1.c *** empty log message *** Nov 26, 2009
search_seeded_phase2.c *** empty log message *** Nov 26, 2009
search_seeded_phase3.c Fixing warnings Dec 15, 2012
search_seeded_phase4.c Fixing warnings Dec 15, 2012
sequence_io.h *** empty log message *** Sep 25, 2009
shmem.cpp *** empty log message *** Sep 2, 2009
shmem.h Added all code coresponding to bowtie2 for LFS. Apr 9, 2014
str_util.h *** empty log message *** Aug 15, 2009
threading.h removed cohort-related files and references; made TBB w/ queue locks … Oct 11, 2016
timer.h trying to bring thread affinitization, various lock types, TBB fully … Mar 20, 2016
tinythread.cpp Added the tiny threads source code and started to change the Makefile… Mar 15, 2013
tinythread.h Added the tiny threads source code and started to change the Makefile… Mar 15, 2013
tokenize.h Small bug fix for SF issue 3054498 Dec 19, 2012
word_io.h fixed mingw failure to compile. Jul 19, 2014
zbox.h Added all code coresponding to bowtie2 for LFS. Apr 9, 2014

README

Bowtie: http://bowtie-bio.sf.net

 - See AUTHORS for information about who wrote Bowtie and its various
   components.
 - See LICENSE for license information.
 - See MANUAL for detailed information on how to use Bowtie.
 - See NEWS for information about changes in this and previous versions
   of Bowtie.
 - See TUTORIAL for a quick example to get you started with Bowtie.