An ultrafast memory-efficient short read aligner
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SeqAn-1.1 trying to bring thread affinitization, various lock types, TBB fully … Mar 20, 2016
doc Add an update to recent news announcing the re-release of v1.2.2 Dec 12, 2017
genomes *** empty log message *** Jan 14, 2009
indexes *** empty log message *** Sep 7, 2010
reads Add support for interleaved fastq Jun 5, 2017
scripts Fix simple color-reads test Oct 18, 2017
third_party release 1.0.1 Mar 20, 2014
.gitignore add some test by-products to gitignore Jul 22, 2017
.travis.yml fix CI test failures Dec 20, 2016
AUTHORS Updates for v1.0.0 release Apr 9, 2013
LICENSE Update license to Artistic License 2.0 Nov 7, 2017
MANUAL Update documentation for v1.2.2 Dec 11, 2017
MANUAL.markdown Fix formatting issue (Issue #62) Sep 13, 2017
Makefile Use TBB's remote filename as argument to tar Dec 11, 2017
NEWS Add an update to recent news announcing the re-release of v1.2.2 Dec 12, 2017
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 v1.2.2 Dec 11, 2017
aligner.h Fix # alignments reported for paired-end, and exiting after -u (PR #65) Nov 1, 2017
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 bringing over some bowtie2 alphabet tables in support of sstring.h Mar 13, 2017
alphabet.h bringing over some bowtie2 alphabet tables in support of sstring.h Mar 13, 2017
assert_helpers.h *** empty log message *** Aug 27, 2010
auto_array.h *** empty log message *** Oct 21, 2009
binary_sa_search.h Working on debugging errors. Most currently comming from integration … Feb 7, 2017
bitpack.h Streamlining and slimming down the contents of the bowtie module in p… Aug 13, 2008
bitset.h Make Bitset classes 32 and 64 bit compatible Nov 17, 2017
blockwise_sa.h allow compilation w/ both c++03 and c++11 May 9, 2018
bowtie Minor tweak to logic for detecting index type Dec 12, 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 remove several vestigial arguments Aug 2, 2017
bowtie_main.cpp many changes that fix LFS bugs and make implicit casts explicit Jun 25, 2014
btypes.h Make Bitset classes 32 and 64 bit compatible Nov 17, 2017
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 fix sPrimeSz indexing Jun 7, 2017
ebwt.cpp test updates Apr 22, 2014
ebwt.h Fix isa return type Sep 5, 2018
ebwt_build.cpp Default bmaxDivN to 4 * nthreads Jun 6, 2017
ebwt_search.cpp Fix segfault when iterating over the list pthreads to join Dec 12, 2017
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 Add support for reordering SAM output Nov 10, 2017
formats.h Add support for interleaved fastq Jun 5, 2017
hit.cpp Add support for reordering SAM output Nov 10, 2017
hit.h Remove reorder functionality Jan 25, 2018
hit_set.cpp *** empty log message *** Nov 24, 2009
hit_set.h remove several vestigial arguments Aug 2, 2017
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 Remove unused variable Dec 11, 2017
pat.cpp Fix issue of reads getting skipped when split across multiple input f… Nov 15, 2017
pat.h Fix issue of reads getting skipped when split across multiple input f… Nov 15, 2017
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 harmonize RandomSource with bowtie2 Mar 13, 2017
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
row_chaser.h Fix issue #35 where bowtie to outputs incorrect results when aligning… Oct 31, 2017
sam.cpp Remove reorder functionality Jan 25, 2018
sam.h Add support for reordering SAM output Nov 10, 2017
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 Add --no-unal option to stop reporting of unaligned reads Jun 5, 2017
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
sstring.h Improve performance of --reorder by emulating move semantics Nov 21, 2017
str_util.h *** empty log message *** Aug 15, 2009
threading.h fix busy-waiting master thread Jul 22, 2017
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 Working on debugging errors. Most currently comming from integration … Feb 7, 2017

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.