A fast and sensitive gapped read aligner
C++ Perl Python Shell C Makefile Objective-C
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doc updated contributors; removed cruft Dec 31, 2016
example Changing my email address Dec 18, 2012
scripts Add support for interleaved FASTQ reads (--12) Jan 27, 2017
third_party A few minor corrections. Feb 7, 2014
.gitignore ignore pyc and swp files Oct 13, 2016
.travis.yml Temporarily remove random test from build script Dec 8, 2016
AUTHORS Updated the AUTHORS with tinythread API author. Feb 21, 2013
LICENSE Removed defunct project files, added README and renamed COPYING to LI… Dec 21, 2012
MANUAL Update documentation for rel2.3.0 Dec 14, 2016
MANUAL.markdown Update documentation for rel2.3.0 Dec 14, 2016
Makefile Use of ANSI C++ when compiling on Windows Dec 22, 2016
NEWS Update rel2.3 documentation Dec 30, 2016
README Removed defunct project files, added README and renamed COPYING to LI… Dec 21, 2012
TUTORIAL Updated TUTORIAL to point to MANUAL Oct 16, 2011
VERSION Update documentation for rel2.3.0 Dec 14, 2016
aligner_bt.cpp Changing my email address Dec 18, 2012
aligner_bt.h Changing my email address Dec 18, 2012
aligner_cache.cpp Added back tinythreads sources and prepared the Makefile for conditio… Jun 16, 2015
aligner_cache.h closer to a working 64-bit implementation. this version is not there … Nov 16, 2013
aligner_driver.cpp Toward more flexible seed placement Apr 4, 2013
aligner_driver.h Toward more flexible seed placement Apr 4, 2013
aligner_metrics.h Changing my email address Dec 18, 2012
aligner_report.h Changing my email address Dec 18, 2012
aligner_result.cpp bug fix and changes to test scripts to reflect lack of colorspace Mar 16, 2016
aligner_result.h Very minor fix involving trim length in getExtendedCoords function Dec 6, 2016
aligner_seed.cpp removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
aligner_seed.h adding extra seed-hit output Sep 8, 2014
aligner_seed2.cpp removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
aligner_seed2.h removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
aligner_seed_policy.cpp Proposal to avoid --local followed by -N reset the seed len to 22, which Jun 25, 2015
aligner_seed_policy.h Fix for non TBB version. Jul 11, 2015
aligner_sw.cpp closer to a working 64-bit implementation. this version is not there … Nov 16, 2013
aligner_sw.h Separate --log-dp and --log-dp-opp output files for extending seed hi… May 30, 2013
aligner_sw_common.h removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
aligner_sw_driver.cpp closer to a working 64-bit implementation. this version is not there … Nov 16, 2013
aligner_sw_driver.h Compilable version for LFS. Nov 14, 2013
aligner_sw_nuc.h Changing my email address Dec 18, 2012
aligner_swsse.cpp Changing my email address Dec 18, 2012
aligner_swsse.h added the latest updates for proposal Feb 21, 2013
aligner_swsse_ee_i16.cpp removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
aligner_swsse_ee_u8.cpp removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
aligner_swsse_loc_i16.cpp Changing my email address Dec 18, 2012
aligner_swsse_loc_u8.cpp removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
aln_sink.cpp A few modifications to --mapq-extra mode, and changed value reported … May 24, 2013
aln_sink.h committing progress toward batched parsing. seems to work for FASTQ a… May 12, 2016
alphabet.cpp removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
alphabet.h removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
assert_helpers.h Changing my email address Dec 18, 2012
banded.cpp Changing my email address Dec 18, 2012
banded.h tthreads work and updated the version. Feb 21, 2013
binary_sa_search.h closer to a working 64-bit implementation. this version is not there … Nov 16, 2013
bitpack.h Changing my email address Dec 18, 2012
blockwise_sa.h fix warnings in parallel index building code when compiling debug tar… Dec 6, 2016
bowtie2 Handle compressed read files when -U is omitted Jan 3, 2017
bowtie2-build Added --debug to inspect wrapper, fixed log message and assure inspec… Feb 6, 2014
bowtie2-inspect Added --debug to inspect wrapper, fixed log message and assure inspec… Feb 6, 2014
bowtie_build_main.cpp Changing my email address Dec 18, 2012
bowtie_main.cpp Changing my email address Dec 18, 2012
bt2_build.cpp reduce the scope of bmaxDivNSet flag Dec 8, 2016
bt2_dp.cpp removing vestiges of long-deprecated --nospin option Nov 27, 2015
bt2_idx.cpp PArtially unified IO error handling for conditional compiled units. Nov 27, 2013
bt2_idx.h Parallelized three time-consuming steps of the index building, with t… Dec 19, 2015
bt2_inspect.cpp Fixed the dealloc Dec 6, 2016
bt2_io.cpp fixed rewind of null pointer Apr 30, 2014
bt2_search.cpp Add support for interleaved FASTQ reads (--12) Jan 27, 2017
bt2_search.h proposed TBB 4.4 fixes. problem seems to have started with 4.4 update 1 Mar 15, 2016
bt2_util.cpp closer to a working 64-bit implementation. this version is not there … Nov 16, 2013
btypes.h Added the 2 binaries types building option with 2 corresponding ebwt… Nov 19, 2013
ccnt_lut.cpp Changing my email address Dec 18, 2012
cpu_numa_info.cpp fixing cohort-locking bug with thread migration. removing dependence … Mar 24, 2016
cpu_numa_info.h fixing cohort-locking bug with thread migration. removing dependence … Mar 24, 2016
diff_sample.cpp Changing my email address Dec 18, 2012
diff_sample.h bug fix and changes to test scripts to reflect lack of colorspace Mar 16, 2016
dp_framer.cpp removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
dp_framer.h removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
ds.cpp Integrating tinythreads into bowtie. Feb 21, 2013
ds.h put all memory tally merging into ifdef USE_MEM_TALLY Aug 25, 2015
edit.cpp Changing my email address Dec 18, 2012
edit.h Changing my email address Dec 18, 2012
endian_swap.h closer to a working 64-bit implementation. this version is not there … Nov 16, 2013
fast_mutex.h Added back tinythreads sources and prepared the Makefile for conditio… Jun 16, 2015
filebuf.h first cut at refactoring code so fastq parsing is divided into two pi… Mar 17, 2016
formats.h Add support for interleaved FASTQ reads (--12) Jan 27, 2017
group_walk.cpp Changing my email address Dec 18, 2012
group_walk.h closer to a working 64-bit implementation. this version is not there … Nov 16, 2013
ival_list.cpp Changing my email address Dec 18, 2012
ival_list.h Changed naming of some member functions to be more consistent. Starti… Jan 22, 2013
limit.cpp Changing my email address Dec 18, 2012
limit.h Changing my email address Dec 18, 2012
ls.cpp Changing my email address Dec 18, 2012
ls.h Changed many data structures required to implement LFS. Nov 11, 2013
mask.cpp Changing my email address Dec 18, 2012
mask.h Changing my email address Dec 18, 2012
mem_ids.h Changing my email address Dec 18, 2012
mm.h Some code cleaning. Feb 13, 2014
multikey_qsort.cpp Changed many data structures required to implement LFS. Nov 11, 2013
multikey_qsort.h Fixed a case the parallelized indexing hangs when indexing a very sma… Jan 26, 2016
opts.h committing progress toward batched parsing. seems to work for FASTQ a… May 12, 2016
outq.cpp Integrating tinythreads into bowtie. Feb 21, 2013
outq.h added the latest updates for proposal Feb 21, 2013
pat.cpp Prevent aligner from failing when given empty FASTQ read files Feb 8, 2017
pat.h Add support for interleaved FASTQ reads (--12) Jan 27, 2017
pe.cpp Changing my email address Dec 18, 2012
pe.h Changing my email address Dec 18, 2012
presets.cpp Pre-2.0.5 release changes, most of which address warnings when g++ is… Jan 5, 2013
presets.h Changing my email address Dec 18, 2012
processor_support.h Fix __cpuid() argument type Oct 25, 2015
pthreadGC2.dll Initial import of Bowtie2 trunk Mar 12, 2011
qual.cpp Changing my email address Dec 18, 2012
qual.h Changing my email address Dec 18, 2012
random_source.cpp Changing my email address Dec 18, 2012
random_source.h closer to a working 64-bit implementation. this version is not there … Nov 16, 2013
random_util.cpp Changing my email address Dec 18, 2012
random_util.h closer to a working 64-bit implementation. this version is not there … Nov 16, 2013
read.h fix issues related to empty reads Oct 20, 2016
read_qseq.cpp fix paired-end qseq parsing Oct 26, 2016
ref_coord.cpp Changing my email address Dec 18, 2012
ref_coord.h Changed naming of some member functions to be more consistent. Starti… Jan 22, 2013
ref_read.cpp removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
ref_read.h Cleaned code and last minor fixes. Feb 14, 2014
reference.cpp fixing some unused variables Jul 5, 2015
reference.h added binary search to reference.cpp's getStretch Apr 2, 2014
sam.cpp revamped --mapq-extra mode so that everything important is in ZT:Z Dec 6, 2016
sam.h removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
scoring.cpp removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
scoring.h tweak default local --min-score; still outstanding: fix so it matches… Dec 6, 2016
search_globals.h removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
sequence_io.h Changing my email address Dec 18, 2012
shmem.cpp Changing my email address Dec 18, 2012
shmem.h Changed many data structures required to implement LFS. Nov 11, 2013
simple_func.cpp Pre-2.0.5 release changes, most of which address warnings when g++ is… Jan 5, 2013
simple_func.h add alwaysPositive member for checking if --score-min is incompatible… Dec 6, 2016
sse_util.cpp Changing my email address Dec 18, 2012
sse_util.h put all memory tally merging into ifdef USE_MEM_TALLY Aug 25, 2015
sstring.cpp bug fix and changes to test scripts to reflect lack of colorspace Mar 16, 2016
sstring.h fixed VectorPatternSource, regorganized tests so file format tests ar… Oct 17, 2016
str_util.h Changing my email address Dec 18, 2012
threading.h removed redundant if/endif fixing NO_QUEUELOCK=1 compile error Oct 10, 2016
timer.h added an optional fine-grained timer Jul 3, 2015
tinythread.cpp Added back tinythreads sources and prepared the Makefile for conditio… Jun 16, 2015
tinythread.h Added back tinythreads sources and prepared the Makefile for conditio… Jun 16, 2015
tokenize.h Fixed SF issue 3054498 Dec 19, 2012
unique.cpp Changing my email address Dec 18, 2012
unique.h Fix git config params tu suppress warnings. Jan 11, 2013
util.h Changing my email address Dec 18, 2012
word_io.h Cleaned code and last minor fixes. Feb 14, 2014
zbox.h Changed many data structures required to implement LFS. Nov 11, 2013

README

Bowtie 2: http://bowtie-bio.sf.net/bowtie2

 - See AUTHORS for information about who wrote Bowtie 2 and its various
   components.
 - See LICENSE for license information.
 - See MANUAL for detailed information on how to use Bowtie 2.
 - See NEWS for information about changes in this and previous versions
   of Bowtie 2.