目录
- .githubReduce the number of outerloop iterations when running random tests4年前
- docMerge branch 'bug_fixes'4年前
- genomes*** empty log message ***17年前
- indexes*** empty log message ***15年前
- readsAdd support for interleaved fastq8年前
- scriptsUpdate path to ar binary and remove c++98 standard requirement4年前
- .gitignoreadd some test by-products to gitignore8年前
- .travis.ymlMerge branch 'bug_fixes'4年前
- AUTHORSUpdates for v1.0.0 release12年前
- LICENSEUpdate license to Artistic License 2.08年前
- MANUALUpdate documentation5年前
- MANUAL.markdownFix UTF-8 characters in website5年前
- MakefileMerge branch 'bug_fixes'4年前
- NEWSUpdate documentation in preparation for release 1.3.14年前
- READMEAdded README and renamed COPYING to LICENSE to be more GitHub-friendly.13年前
- TUTORIALfixing e coli link and instructions9年前
- VERSIONUpdate documentation in preparation for release 1.3.14年前
- aligner.hUse EList instead of std::vector5年前
- aligner_0mm.hFix additional warnings5年前
- aligner_1mm.hUse EList instead of std::vector5年前
- aligner_23mm.hUse EList instead of std::vector5年前
- aligner_metrics.hCode consolidation5年前
- aligner_seed_mm.hUse EList instead of std::vector5年前
- alphabet.cppuse signed char for mask2iupac to avoid error on aarch645年前
- alphabet.huse signed char for mask2iupac to avoid error on aarch645年前
- assert_helpers.hCode consolidation5年前
- binary_sa_search.hUse EList instead of std::vector5年前
- bitpack.hStreamlining and slimming down the contents of the bowtie module in preparation for the 1.0 release17年前
- bitset.hMake Bitset classes 32 and 64 bit compatible8年前
- blockwise_sa.hRemove temp logs and reenable simple tests for s390x5年前
- bowtieClean up bowtie script5年前
- bowtie-buildCode consolidation5年前
- bowtie-inspectRemove unused import5年前
- bowtie_build_main.cppUse EList instead of std::vector5年前
- bowtie_inspect.cppUse EList instead of std::vector5年前
- bowtie_main.cppUse EList instead of std::vector5年前
- bt2_locks.cppFix issue that may cause deadlocks when using MCS lock with many threads4年前
- bt2_locks.hFix issue that may cause deadlocks when using MCS lock with many threads4年前
- btypes.hMake Bitset classes 32 and 64 bit compatible8年前
- ccnt_lut.cpp*** empty log message ***16年前
- chaincat.cpp*** empty log message ***16年前
- cpu_numa_info.cppgetting rid of dependence on libnuma9年前
- cpu_numa_info.hgetting rid of dependence on libnuma9年前
- diff_sample.hFix issues discovered during testing5年前
- ds.hUse EList instead of vector for read buffers, get rid of redundant auto_array5年前
- ebwt.cppInclude bt2 indexes in index search7年前
- ebwt.hFix an overflow issue that would corrupt the index created by bowtie-build #1244年前
- ebwt_build.cppFix the output of EBWT restore check4年前
- ebwt_search.cppMake it an error to use --reorder and not specify -S5年前
- ebwt_search.htrying to bring thread affinitization, various lock types, TBB fully over from Bowtie29年前
- ebwt_search_backtrack.hUse EList instead of std::vector5年前
- ebwt_search_util.cppUse EList instead of std::vector5年前
- ebwt_search_util.hFix compiler warning4年前
- edit.cpp*** empty log message ***16年前
- edit.h*** empty log message ***16年前
- endian_swap.hIn work. From this point we temporarly break bowtie functionality.12年前
- fast_mutex.hAdded the tiny thread spinlock and started the tiny thread usage implementation changes.13年前
- filebuf.hFix issues detected by random-test5年前
- formats.hCode consolidation5年前
- hit.cppRemove extra quote in include directive5年前
- hit.hFix an issue causing bowtie to output incorrect XM:i value for certain reads #1274年前
- hit_set.cppUse EList instead of std::vector5年前
- hit_set.hUse EList instead of std::vector5年前
- log.cpp*** empty log message ***16年前
- log.htrying to bring thread affinitization, various lock types, TBB fully over from Bowtie29年前
- ls.cppUse EList instead of std::vector5年前
- ls.hCode consolidation5年前
- mem_ids.hFix an overflow issue that would corrupt the index created by bowtie-build #1244年前
- mm.hBuffered all file access (originally suggested by James)11年前
- multikey_qsort.hImprove speed of bowtie-build sanity checking4年前
- pat.cppUse EList instead of std::vector5年前
- pat.hSmall improvements to reorder algorithm5年前
- pool.hUse EList instead of std::vector5年前
- processor_support.hReplace non-ascii double quotes and delete trailing whitespace5年前
- qual.cpp*** empty log message ***16年前
- qual.hCode consolidation5年前
- random_source.hharmonize RandomSource with bowtie28年前
- random_test.cpp*** empty log message ***16年前
- range.hUse EList instead of std::vector5年前
- range_cache.hFix unused variable warnings5年前
- range_chaser.hback out range chaser fix5年前
- range_source.hConvert query characters to ASCII when printing backtrack5年前
- read.hFix unused variable warnings5年前
- ref_aligner.cpp*** empty log message ***17年前
- ref_aligner.hUse EList instead of std::vector5年前
- ref_read.cppUse EList instead of std::vector5年前
- ref_read.hUse EList instead of std::vector5年前
- reference.hUse EList instead of std::vector5年前
- row_chaser.hCode consolidation5年前
- sam.cppSmall improvements to reorder algorithm5年前
- sam.hFix additional warnings5年前
- search_1mm_phase1.c*** empty log message ***16年前
- search_1mm_phase2.c*** empty log message ***16年前
- search_23mm_phase1.c*** empty log message ***16年前
- search_23mm_phase2.c*** empty log message ***16年前
- search_23mm_phase3.cFixing warnings13年前
- search_exact.cCode consolidation5年前
- search_globals.hInitial colorspace deprecation5年前
- search_seeded_phase1.cCode consolidation5年前
- search_seeded_phase2.cUse EList instead of std::vector5年前
- search_seeded_phase3.cUse EList instead of std::vector5年前
- search_seeded_phase4.cCode consolidation5年前
- sequence_io.hRemove unneeded call to close function5年前
- shmem.cpp*** empty log message ***16年前
- shmem.hFix compiler warnings4年前
- sstring.hFix the output of EBWT restore check4年前
- str_util.h*** empty log message ***16年前
- threading.hFix build issues when compiling with C++98 standard or earlier.4年前
- timer.htrying to bring thread affinitization, various lock types, TBB fully over from Bowtie29年前
- tinythread.cppDo not include the contents of threading.cpp when compiling with C++11 or newer.4年前
- tinythread.hAdded the tiny threads source code and started to change the Makefile for minGw build.13年前
- tokenize.hUse EList instead of std::vector5年前
- util.hFix compiler warnings4年前
- word_io.hfixed mingw failure to compile.11年前
- zbox.hUse EList instead of std::vector5年前
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