zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
941 Commits
3 Branches
0 Tags
123 MiB
Commit Graph

941 Commits (e43eace9e5ef13f128bf36e413883ff8fcd3c9bf)

Author SHA1 Message Date
Nils Homer e43eace9e5 Update bwa.1 2022-02-18 13:36:09 -08:00
Heng Li d587a9561b fixed wrong Markdown format in README 2021-05-10 12:48:45 -04:00
Heng Li b1ab735f7c updated to Github CI status 2021-05-10 12:47:13 -04:00
Heng Li 7fe5a14058 Merge pull request #325 from jmarshall/ci 
Use GitHub Actions instead of Travis CI
 2021-05-10 12:44:43 -04:00
John Marshall d27d6a520b Convert Travis CI to GitHub Actions 
Make an equivalent GitHub Actions workflow that tests compilation
with both GCC and Clang.
 2021-05-09 22:54:58 +01:00
Heng Li 87e42dbe32 added code of conduct 2021-04-22 17:35:37 -04:00
Heng Li ddbd5f7fb7 Removed the debug output; resolves #320 2021-03-09 08:56:52 -05:00
Heng Li 5b96937edc deprecate bwasw 2021-03-09 00:52:20 -05:00
Heng Li e2dbfe60e3 output more memory information 2021-02-23 10:43:41 -05:00
Heng Li d422bdbed9 debug flag to measure memory 2021-02-22 23:26:03 -05:00
Heng Li 94ff6b297a added the MIT license header to main.c 2020-07-02 13:49:42 -04:00
Heng Li d13c2af9bd Merge branch 'master' of github.com:lh3/bwa 2020-07-01 23:02:31 -04:00
Heng Li 02a9add042 added MIT license to some non-GPL source files 2020-07-01 23:02:01 -04:00
Heng Li 3112df7100 Merge pull request #267 from SoapGentoo/fixes 
GCC 10 and Makefile fixes
 2020-03-23 08:56:40 -04:00
David Seifert 2f82fe897a Fix building against GCC 10 
* GCC 10 defaults to `-fno-common`, which makes C behave
  more like C++ in that you can only ever have one definition
  of an object per executable.
 2020-02-26 13:24:17 +01:00
Heng Li e8e2803a3d updated badges 2019-07-09 15:44:34 -04:00
Heng Li 9b12309015 mention bwa-mem2 2019-07-09 10:25:57 -04:00
Heng Li cd29a7cb54 r1198: exit if .alt is malformatted 
Resolves #232
 2019-01-23 13:28:11 -05:00
Heng Li e4d7a94252 Merge remote-tracking branch 'origin/master' 2018-04-10 15:01:35 -04:00
Heng Li f9294c0593 Merge pull request #190 from ihaque-freenome/bwa-postalt-fix 
Bug/patch: bwa-postalt.js writes invalid output for SAM input that is an exact multiple of 65536 bytes in length
 2018-04-07 18:03:10 -04:00
Imran Haque 27dd1da702 Exclude empty SAM lines in bounds check for ALT postprocessor 2018-04-07 07:47:32 +00:00
Heng Li 11d53b06fb Merge branch 'dev' into XB 2018-04-02 10:47:45 -04:00
Heng Li eb7dbc1429 optionally write XB to include alignment score 
request from 4DN-DCIC
 2018-04-02 10:43:41 -04:00
Heng Li fde1fd7ce3 emphasize pacbio and nanopore 2017-11-06 19:51:01 -05:00
Heng Li eef04271e6 wording changes 2017-11-06 19:49:19 -05:00
Heng Li 1a2b0c001a fixed a typo in link 2017-11-06 19:43:02 -05:00
Heng Li 824e00e7ac formatting change 2017-11-06 19:41:53 -05:00
Heng Li ab64326ae6 claim bwa-mem long-read mode deprecated 2017-11-06 19:40:42 -05:00
Heng Li 9f26bfcc77 Released bwa-0.7.17 (r1188) 2017-10-23 13:10:17 -04:00
Heng Li b582816211 r1187: a typo in command line help 2017-09-26 09:35:19 -04:00
Heng Li 340babdd67 r1185: don't lower supp mapq with -5 2017-09-11 09:58:41 -04:00
Heng Li a9c688ac92 r1181: fixed a segfault (#145) due to (#138) 2017-07-31 07:55:35 -04:00
Heng Li 47d9fb27d7 Release 0.7.16-r1180 2017-07-30 22:35:38 -04:00
Heng Li 5d15c8b09f Merge pull request #129 from lexentbio/bwakit_fix_sort 
Fix output file parameter for samtools sort
 2017-07-30 19:14:09 -04:00
Heng Li 950ea8cf40 Merge pull request #138 from nh13/nh_mem_mate_cigar 
Mem should set the mate cigar tag.
 2017-07-30 19:05:47 -04:00
Heng Li 83260ccb10 Merge pull request #60 from jdagilliland/typo 
Typos, doc improvements in man page
 2017-07-30 18:59:11 -04:00
Heng Li 1eee77ad93 Merge pull request #84 from jblachly/readgroupfix 
Forbid literal TAB control characters in @RG line
 2017-07-30 18:56:39 -04:00
Heng Li 24a8d66481 removed drone.io 2017-07-30 18:49:06 -04:00
Heng Li 89a5c0c5c8 moved BWTFree() into BWTIncFree() 
BWTFree() is not for build. Only BWTIncFree() is needed.
 2017-07-30 18:47:03 -04:00
Heng Li 0976272d99 Merge pull request #139 from jmarshall/fixes 
Various collected fixes (updated versions of several existing PRs)
 2017-07-30 18:36:07 -04:00
Heng Li a54e76945e Merge pull request #70 from rmzelle/patch-1 
Update README.md
 2017-07-30 17:01:27 -04:00
Heng Li 31bf49d814 Merge pull request #96 from jpfeil/master 
Add -M option to run-bwamem
 2017-07-30 16:57:30 -04:00
Heng Li 498973642f Merge pull request #123 from bwlang/patch-1 
updates grch38 URL
 2017-07-30 16:55:39 -04:00
Heng Li 87ed015b24 Merge pull request #141 from jmarshall/bwasw-nan 
Fail to infer insert size distribution when no pairs are within boundaries (re issue 108)
 2017-07-30 16:53:04 -04:00
Andreas Tille c56c2e4677 Several trivial Debian patches 
[Andreas Tille]
Check exact number of arguments of bwtupdate
Fix spelling

[Fabian Klötzl]
change printing as size_t is unsigned
 2017-07-04 21:24:15 +01:00
Nils Homer 3b96dcee7f Mem should set the mate cigar tag. 2017-07-03 08:51:00 -07:00
John Marshall bcb475cd03 In bsw2_stat(), fail to infer when no pairs are within boundaries 
Just as we set r.failed and return early if there are no high-quality
read pairs at all, also do so if there are none within the calculated
boundaries.  This avoids returning avg=NAN std=NAN, which leads to
malloc(INFINITY) and a crash; fixes #108.
 2017-07-03 13:42:11 +01:00
John Marshall 690649872b Copy the whole kstring_t even if it contains NULs 
FASTQ files containing NULs are invalid but should not cause bwa to
crash, as it does if the quality line contains a NUL.  Fixes #122.
 2017-06-30 12:46:56 +01:00
John Marshall a61b1dc610 Expand tot_seqs variable to long long 
This counter is only used in a log message.  Fixes #131.
 2017-06-29 15:36:46 +01:00
Rintze M. Zelle 5ede7eb981 Update README.md 
Correct header formatting, fix some typos in headers
 2017-06-28 12:07:27 +01:00