4820d8fc32
Merge branch 'dev'
2016-02-23 10:40:26 -05:00
9a828344ec
moved indexing to libbwa
2016-02-13 18:48:46 -05:00
099c24f5fc
fix assertion failure report on bio-bwa-help mailing list
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bwase.c:180: bwa_refine_gapped_core: Assertion `re - rb == rlen' failed
2016-02-11 14:00:18 +00:00
cc9eef2d33
Merge branch 'dev'
2016-02-01 11:57:56 -05:00
86170ffd2f
r1102: resumed versioning
2016-02-01 11:57:14 -05:00
25097a9a88
Merge branch 'dev'
2016-02-01 11:52:02 -05:00
ede7b092a2
updated GRCh38 download link
2016-02-01 11:50:25 -05:00
1e6a10ce2d
a typo in fastmap command-line prompt
2016-02-01 11:41:46 -05:00
6f0ea0b7e3
use /usr/bin/env perl
2016-02-01 11:39:50 -05:00
fdf47000e7
integer overflow on indexing
2016-01-26 23:21:23 -05:00
c819643412
make kthread.c compiled with g++
2016-01-26 22:49:28 -05:00
1247dc2346
removed the pbread mode
...
It is not working well. Not at all.
2016-01-26 22:37:01 -05:00
616a53491d
Merge branch 'dev' of github.com:lh3/bwa into dev
2016-01-26 17:19:16 -05:00
feeb41f42d
updated dependencies
2016-01-26 13:54:47 -05:00
be2020c4af
ropebwt2 for bwt construction
2016-01-26 13:46:08 -05:00
1b2e9a6d89
Merge pull request #51 from sethbrin/master
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update the usage of main_fastmap
2016-01-21 14:10:32 -05:00
1ec736e06a
Merge pull request #50 from mgymrek/patch-1
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Editing URL for b38 download
2016-01-20 09:58:59 -05:00
176a7ec67e
update the usage of main_fastmap
2016-01-20 22:52:25 +08:00
9be943cec0
Editing URL for b38 download
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The previous link appears to no longer exist.
2016-01-17 10:58:02 -05:00
f9ce2a6c73
fix a bug where bwa_sa2pos could return without setting strand
2015-12-11 09:29:27 +00:00
e3ea2a8222
Merge pull request #47 from mfcovington/feature/fix-maxk-error
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Include 'unistd.h' to explicitly declare 'getopt'
2015-11-14 20:47:22 -05:00
c2efebefa7
Include 'unistd.h' to explicitly declare 'getopt'
2015-11-14 17:27:57 -08:00
0911122749
Merge branch 'master' of github.com:lh3/bwa
2015-08-27 10:44:55 -04:00
e8d531189f
Merge branch 'dev'
2015-08-27 10:44:34 -04:00
6c668d3e1a
fixed a bug in reverse-complement
2015-08-27 10:44:08 -04:00
9812521922
Merge pull request #43 from wookietreiber/perl-shebangs
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use more portable /usr/bin/env perl for scripts
2015-07-02 11:52:40 -04:00
b1a96f58b6
use more portable /usr/bin/env perl for scripts
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This is useful, e.g. if your perl is not installed in `/usr/bin` or you
want to give a specific perl precendence over the one installed in
`/usr/bin`. The `-w` is not needed since there is also `use warnings;`
in these scripts.
2015-07-02 15:23:40 +02:00
eb428d7d31
Merge branch 'dev'
2015-03-25 12:18:22 -04:00
3ae437ac13
r1044: fixed an out-of-order bug in kthread
2015-03-25 12:16:06 -04:00
163f949a33
added maxk: max unique k-mer at each position
2015-02-08 16:49:25 -05:00
1e29bccc65
Merge branch 'dev'
2014-12-29 16:43:42 -05:00
1f99921b73
changed download link: 0.7.11 => 0.7.12
2014-12-29 16:43:22 -05:00
5a340797e7
Merge branch 'dev'
2014-12-28 15:45:11 -05:00
8211fbcb62
Released 0.7.12
2014-12-28 15:44:59 -05:00
e746a3eac7
r1038: wrong 0x100|0x800 flags in PE mode
2014-12-24 13:22:46 -05:00
3ae8d4b80b
r1037: wrong read number flag
2014-12-24 00:55:33 -05:00
b9bbf2d3df
r1036: PE ALT mapping incorrect
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No SA/XA tags!
2014-12-24 00:49:50 -05:00
b8e189c1e5
Merge branch 'dev'
2014-12-23 15:29:34 -05:00
408fd5e072
Released bwa-0.7.11-r1034
2014-12-23 15:29:18 -05:00
d7ce7e1395
hs38D1=>hs38DH; cmd help for run-gen-ref
2014-12-23 11:48:59 -05:00
ed95769a33
updated documentations
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(prepare for release)
2014-12-21 16:30:29 -05:00
c05a721f28
improved doc and don't type HLA by default
2014-12-21 00:12:11 -05:00
5aba188969
write empty .gt file as a placeholder
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to suppress error messages from run-bwamem
2014-12-20 22:27:27 -05:00
32c4e3fe5a
updated decoy sequences and names
2014-12-20 22:24:13 -05:00
4ffdc7b5ad
Merge branch 'dev'
2014-12-19 07:50:23 -05:00
c561759222
r1027: segfault caused by the last commit
2014-12-12 16:56:54 -05:00
4e705c037e
Merge branch 'dev'
2014-12-11 10:39:04 -05:00
925ddfb697
r1025: accept file with -H; allow to replace @SQ
2014-12-11 10:38:36 -05:00
139df93af9
Merge branch 'dev'
2014-12-10 23:21:13 -05:00
efa0dd561a
wrong sentence in README-alt
2014-12-10 23:20:46 -05:00
Heng Li
Steven Leonard
zengping
Melissa Gymrek
Mike Covington
Christian Krause