d6636daead
Include in man page info on read types
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Previously this info had only been present in the help text emitted from
`bwa mem` without arguments, but I think it helpful to include in man page.
2016-03-31 12:40:09 -04:00
e10fc577e1
Fix a few typos in man page
2016-03-31 12:40:03 -04:00
bb7533e32c
Merge pull request #55 from jdagilliland/master
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Minor doc fix
2016-03-17 12:15:12 -04:00
6460ef5572
Minor doc fix
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MAN page described `bwa mem` option `-D` variously as integer and float,
when it is in fact a float.
2016-03-17 12:00:47 -04:00
2c078eb667
option to skip ALT
2016-03-16 16:06:49 -04:00
83662032a2
Merge branch 'dev'
2016-02-23 11:24:40 -05:00
9e5852c540
Released bwa-0.7.13 (r1126)
2016-02-23 11:24:19 -05:00
67aa1ca731
Merge branch 'dev'
2016-02-23 11:17:21 -05:00
b94a78adbf
use /usr/env/perl
2016-02-23 11:08:43 -05:00
f1ce529cd9
added comment
2016-02-23 11:08:11 -05:00
11437a14f4
Port #48 to the dev branch
2016-02-23 11:07:27 -05:00
5ecdc66e46
Merge branch 'master' of github.com:lh3/bwa
2016-02-23 11:05:47 -05:00
f9a7869079
Merge pull request #48 from srl147/master
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ensure bwa_sa2pos does not return without setting strand
2016-02-23 11:05:35 -05:00
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
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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
Jason Gilliland
Heng Li
Steven Leonard
zengping
Melissa Gymrek
Mike Covington
Christian Krause