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Author SHA1 Message Date
Heng Li d26eb2d288 Merge pull request #330 from nh13/patch-4 
Add the mate mapping quality tag
 2022-03-06 18:07:01 -05:00
Heng Li 4a18837bd2 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 d47f12cddc 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 e43eace9e5 Update bwa.1 2022-02-18 13:36:09 -08:00
Nils Homer 56026158d8 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 f5e83701ab Add the mate mapping quality tag 2021-07-21 11:12:27 -07:00
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
Nils Homer b58da139c3 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 34caf50d46 allow the user to specify the XA drop ratio via the -z option 2020-08-12 09:01:44 -07:00
Nils Homer 9cbbd6bf94 Update fastmap.c 2020-08-12 08:51:19 -07:00
Nils Homer f717ea1318 Output mapping quality with XB 2020-08-06 10:10:58 -07:00
Nils Homer 1a11a6f4b9 Document "-u" 2020-08-06 10:08:29 -07:00
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