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
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
e43eace9e5
Update bwa.1
2022-02-18 13:36:09 -08:00
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
d587a9561b
fixed wrong Markdown format in README
2021-05-10 12:48:45 -04:00
b1ab735f7c
updated to Github CI status
2021-05-10 12:47:13 -04:00
7fe5a14058
Merge pull request #325 from jmarshall/ci
...
Use GitHub Actions instead of Travis CI
2021-05-10 12:44:43 -04:00
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
87e42dbe32
added code of conduct
2021-04-22 17:35:37 -04:00
ddbd5f7fb7
Removed the debug output; resolves #320
2021-03-09 08:56:52 -05:00
5b96937edc
deprecate bwasw
2021-03-09 00:52:20 -05:00
e2dbfe60e3
output more memory information
2021-02-23 10:43:41 -05:00
d422bdbed9
debug flag to measure memory
2021-02-22 23:26:03 -05:00
94ff6b297a
added the MIT license header to main.c
2020-07-02 13:49:42 -04:00
d13c2af9bd
Merge branch 'master' of github.com:lh3/bwa
2020-07-01 23:02:31 -04:00
02a9add042
added MIT license to some non-GPL source files
2020-07-01 23:02:01 -04:00
3112df7100
Merge pull request #267 from SoapGentoo/fixes
...
GCC 10 and Makefile fixes
2020-03-23 08:56:40 -04:00
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
e8e2803a3d
updated badges
2019-07-09 15:44:34 -04:00
9b12309015
mention bwa-mem2
2019-07-09 10:25:57 -04:00
cd29a7cb54
r1198: exit if .alt is malformatted
...
Resolves #232
2019-01-23 13:28:11 -05:00
e4d7a94252
Merge remote-tracking branch 'origin/master'
2018-04-10 15:01:35 -04:00
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
27dd1da702
Exclude empty SAM lines in bounds check for ALT postprocessor
2018-04-07 07:47:32 +00:00
11d53b06fb
Merge branch 'dev' into XB
2018-04-02 10:47:45 -04:00
eb7dbc1429
optionally write XB to include alignment score
...
request from 4DN-DCIC
2018-04-02 10:43:41 -04:00
fde1fd7ce3
emphasize pacbio and nanopore
2017-11-06 19:51:01 -05:00
eef04271e6
wording changes
2017-11-06 19:49:19 -05:00
1a2b0c001a
fixed a typo in link
2017-11-06 19:43:02 -05:00
824e00e7ac
formatting change
2017-11-06 19:41:53 -05:00
ab64326ae6
claim bwa-mem long-read mode deprecated
2017-11-06 19:40:42 -05:00
9f26bfcc77
Released bwa-0.7.17 (r1188)
2017-10-23 13:10:17 -04:00
b582816211
r1187: a typo in command line help
2017-09-26 09:35:19 -04:00
340babdd67
r1185: don't lower supp mapq with -5
2017-09-11 09:58:41 -04:00
a9c688ac92
r1181: fixed a segfault ( #145 ) due to ( #138 )
2017-07-31 07:55:35 -04:00
47d9fb27d7
Release 0.7.16-r1180
2017-07-30 22:35:38 -04:00
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
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
83260ccb10
Merge pull request #60 from jdagilliland/typo
...
Typos, doc improvements in man page
2017-07-30 18:59:11 -04:00
1eee77ad93
Merge pull request #84 from jblachly/readgroupfix
...
Forbid literal TAB control characters in @RG line
2017-07-30 18:56:39 -04:00
24a8d66481
removed drone.io
2017-07-30 18:49:06 -04:00
89a5c0c5c8
moved BWTFree() into BWTIncFree()
...
BWTFree() is not for build. Only BWTIncFree() is needed.
2017-07-30 18:47:03 -04:00
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
a54e76945e
Merge pull request #70 from rmzelle/patch-1
...
Update README.md
2017-07-30 17:01:27 -04:00
31bf49d814
Merge pull request #96 from jpfeil/master
...
Add -M option to run-bwamem
2017-07-30 16:57:30 -04:00
498973642f
Merge pull request #123 from bwlang/patch-1
...
updates grch38 URL
2017-07-30 16:55:39 -04:00
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
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
3b96dcee7f
Mem should set the mate cigar tag.
2017-07-03 08:51:00 -07:00
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
Heng Li
Nils Homer
Heng Li
John Marshall
Heng Li
David Seifert
Imran Haque
Andreas Tille
Nils Homer
John Marshall