A fast and sensitive gapped read aligner
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doc Make mention of experimental CMake support Aug 7, 2018
example Add example BAM file Aug 3, 2018
scripts Rename --trim-reads-exceeding-len to --trim-to Aug 7, 2018
third_party A few minor corrections. Feb 7, 2014
.gitignore Ignore sanitized binaries Dec 29, 2017
.travis.yml Attempt at solving travis LSAN failures Jun 15, 2018
AUTHORS Update documentation in preparation for release 2.3.3 Sep 7, 2017
CMakeLists.txt Generate dSYM files when compiling debug binaries in Xcode Aug 7, 2018
LICENSE Removed defunct project files, added README and renamed COPYING to LI… Dec 21, 2012
MANUAL Update documentation for v2.3.4.2 Aug 7, 2018
MANUAL.markdown Update documentation for v2.3.4.2 Aug 7, 2018
Makefile Fix an issue that can cause make to fail when running static-libs recipe Aug 6, 2018
NEWS Make mention of experimental CMake support Aug 7, 2018
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 to v2.3.4.2 Jul 29, 2018
aligner_bt.cpp fixing old edit distance measure to be something more like number of … Sep 28, 2016
aligner_bt.h Changing my email address Dec 18, 2012
aligner_cache.cpp ported stack mutex; removed readsPerBatchOutput option; fixed nthread… May 3, 2017
aligner_cache.h ported stack mutex; removed readsPerBatchOutput option; fixed nthread… May 3, 2017
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 Fix pointer comparison issue #81 May 5, 2017
aligner_result.h Resolves #127: Allow optional use of X and = in CIGAR output Aug 3, 2017
aligner_seed.cpp merging in master Jul 18, 2017
aligner_seed.h Fix additional issues detected by sanitizer Dec 28, 2017
aligner_seed2.cpp removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
aligner_seed2.h merging in rel2.3 Dec 8, 2016
aligner_seed_policy.cpp Initial fix for issue #104 Jul 4, 2017
aligner_seed_policy.h Fix for non TBB version. Jul 11, 2015
aligner_sw.cpp fixing old edit distance measure to be something more like number of … Sep 28, 2016
aligner_sw.h Separate --log-dp and --log-dp-opp output files for extending seed hi… May 30, 2013
aligner_sw_common.h ported stack mutex; removed readsPerBatchOutput option; fixed nthread… May 3, 2017
aligner_sw_driver.cpp merging in master Jul 18, 2017
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 ported stack mutex; removed readsPerBatchOutput option; fixed nthread… May 3, 2017
aligner_swsse_ee_i16.cpp merging in master Jul 18, 2017
aligner_swsse_ee_u8.cpp merging in rel2.3 Dec 8, 2016
aligner_swsse_loc_i16.cpp merging in master Jul 18, 2017
aligner_swsse_loc_u8.cpp merging in master Jul 18, 2017
aln_sink.cpp Add suppport for preserving SAM tags Aug 3, 2018
aln_sink.h Merge branch 'batch_parsing_output' into bug_fixes Aug 24, 2017
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 additional issues detected by sanitizer Dec 28, 2017
bowtie2 Update documentation in preparation for release of v2.3.4 Dec 29, 2017
bowtie2-build Progragate exit status of subprocess to the parent shell #174 Jul 26, 2018
bowtie2-inspect Add missing sys import Aug 16, 2018
bowtie_build_main.cpp Changing my email address Dec 18, 2012
bowtie_main.cpp merging in master Jul 18, 2017
bt2_build.cpp Add support for compressed reference files Aug 28, 2017
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 back out earlier solution; more thorough checking for when to skip fi… Jul 27, 2018
bt2_inspect.cpp Fixed the dealloc Dec 6, 2016
bt2_io.cpp back out earlier solution; more thorough checking for when to skip fi… Jul 27, 2018
bt2_search.cpp Merge branch 'bam_support' into bug_fixes Aug 7, 2018
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 ported stack mutex; removed readsPerBatchOutput option; fixed nthread… May 3, 2017
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 ported stack mutex; removed readsPerBatchOutput option; fixed nthread… May 3, 2017
ds.h Fix additional issues detected by sanitizer Dec 28, 2017
edit.cpp Changing my email address Dec 18, 2012
edit.h Changing my email address Dec 18, 2012
endian_swap.h ported stack mutex; removed readsPerBatchOutput option; fixed nthread… May 3, 2017
fast_mutex.h Added back tinythreads sources and prepared the Makefile for conditio… Jun 16, 2015
filebuf.h Potential fix for issues #155 and #158 Dec 3, 2017
formats.h Working implementation of BAM parser Jul 31, 2018
group_walk.cpp Changing my email address Dec 18, 2012
group_walk.h ported stack mutex; removed readsPerBatchOutput option; fixed nthread… May 3, 2017
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 fix failure to fully sort diff cov sample Jun 8, 2017
opts.h Merge branch 'bam_support' into bug_fixes Aug 7, 2018
outq.cpp Fix a bug causing some SAM records to not be outputted Sep 5, 2017
outq.h fix segfault with --reorder Jan 24, 2018
pat.cpp Add support for paired-end reads Aug 3, 2018
pat.h Merge branch 'bam_support' into bug_fixes Aug 7, 2018
pe.cpp Changing my email address Dec 18, 2012
pe.h Changing my email address Dec 18, 2012
presets.cpp Fix issue causing bowtie2 to crash when using '--fast-local' mode Jun 15, 2018
presets.h Changing my email address Dec 18, 2012
processor_support.h Fix __cpuid() argument type Oct 25, 2015
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 Add suppport for preserving SAM tags Aug 3, 2018
read_qseq.cpp General bugfixes and improvements Sep 20, 2017
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 back out earlier solution; more thorough checking for when to skip fi… Jul 27, 2018
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 Add suppport for preserving SAM tags Aug 3, 2018
sam.h Add suppport for preserving SAM tags Aug 3, 2018
scoring.cpp removing some old vestigates of colorspace and fuzzy-quality modes Mar 16, 2016
scoring.h make default local --score-min match the documentation Oct 1, 2016
search_globals.h put more params in PatternSourceParams Jul 26, 2017
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 fix busy-waiting on worker threads Jul 25, 2017
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 revamped accounting for best and second-best alignment scores; added … Sep 27, 2016
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.