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955 Commits (58e3ed223f6fdb56797d4de94ce1422aeb8408c4)

Author SHA1 Message Date
Heng Li 58e3ed223f Merge branch 'feature/add-xa-drop-ratio-option' of https://github.com/fulcrumgenomics/bwa into fulcrumgenomics-feature/add-xa-drop-ratio-option 2022-03-06 18:21:49 -05:00
Heng Li 41e007868c
Merge pull request #293 from nh13/patch-2 
Output mapping quality with XB
 2022-03-06 18:18:45 -05:00
Heng Li cb7e5dffcf
Merge pull request #292 from nh13/patch-1 
Document "-u"
 2022-03-06 18:16:09 -05:00
Heng Li 40b3aeed56
Merge pull request #297 from nh13/patch-3 
Clarify bwa mem -5 option
 2022-03-06 18:12:09 -05:00
Heng Li 0747fcc09d
Merge pull request #330 from nh13/patch-4 
Add the mate mapping quality tag
 2022-03-06 18:07:01 -05:00
Heng Li ef52b4ac19
Merge pull request #336 from nh13/patch-5 
Add the header line to the output SAM
 2022-03-06 18:06:38 -05:00
Heng Li 760098d1c2
Merge pull request #343 from nh13/patch-7 
Update bwa.1 to remove ancient reference to picard
 2022-03-06 18:05:46 -05:00
Nils Homer 4bf3cdf948
Update bwa.1 2022-02-18 13:36:09 -08:00
Nils Homer 6b18630a62
Add the header line to the output SAM 
In particular, this defines the output SAM to be unsorted BUT also query grouped.  The latter is very important to explicitly define so downstream tools that don't make assumptions know that reads from the same template are grouped.
 2021-12-14 08:02:05 -07:00
Nils Homer d8dd308a1f
Add the mate mapping quality tag 2021-07-21 11:12:27 -07:00
Heng Li 3ddd7b87d4 fixed wrong Markdown format in README 2021-05-10 12:48:45 -04:00
Heng Li fe209ff1ca updated to Github CI status 2021-05-10 12:47:13 -04:00
Heng Li f033d4e4e7
Merge pull request #325 from jmarshall/ci 
Use GitHub Actions instead of Travis CI
 2021-05-10 12:44:43 -04:00
John Marshall 765fac1070 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 fbfffc9031 added code of conduct 2021-04-22 17:35:37 -04:00
Heng Li 34374c5613 Removed the debug output; resolves #320 2021-03-09 08:56:52 -05:00
Heng Li 110bf9b8ed deprecate bwasw 2021-03-09 00:52:20 -05:00
Heng Li f1d1fd7c42 output more memory information 2021-02-23 10:43:41 -05:00
Heng Li b9accf95ad debug flag to measure memory 2021-02-22 23:26:03 -05:00
Nils Homer 84b2abb675
Clarify bwa mem -5 option 
Clarify that the -5 bwa mem option chooses the alignment that starts earliest in the read relative to the read/sequencing order, not genomic coordinate order
 2020-08-18 23:01:43 -07:00
Nils Homer 50122bed2a allow the user to specify the XA drop ratio via the -z option 2020-08-12 09:01:44 -07:00
Nils Homer ab9e0e0226
Update fastmap.c 2020-08-12 08:51:19 -07:00
Nils Homer e050ec9a10
Output mapping quality with XB 2020-08-06 10:10:58 -07:00
Nils Homer e5985723cc
Document "-u" 2020-08-06 10:08:29 -07:00
Heng Li 13b5637fe6 added the MIT license header to main.c 2020-07-02 13:49:42 -04:00
Heng Li c4a010d19f Merge branch 'master' of github.com:lh3/bwa 2020-07-01 23:02:31 -04:00
Heng Li 436aceb4ef added MIT license to some non-GPL source files 2020-07-01 23:02:01 -04:00
Heng Li 3072c80e9c
Merge pull request #267 from SoapGentoo/fixes 
GCC 10 and Makefile fixes
 2020-03-23 08:56:40 -04:00
David Seifert 2a1ae7b6f3
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 3a2b0c05dd updated badges 2019-07-09 15:44:34 -04:00
Heng Li 38e751a40a mention bwa-mem2 2019-07-09 10:25:57 -04:00
Heng Li 20d0a13092 r1198: exit if .alt is malformatted 
Resolves #232
 2019-01-23 13:28:11 -05:00
Heng Li f090f93460 Merge remote-tracking branch 'origin/master' 2018-04-10 15:01:35 -04:00
Heng Li e624290ad4
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