31bf49d814
Merge pull request #96 from jpfeil/master
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Add -M option to run-bwamem
2017-07-30 16:57:30 -04:00
498973642f
Merge pull request #123 from bwlang/patch-1
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updates grch38 URL
2017-07-30 16:55:39 -04:00
87ed015b24
Merge pull request #141 from jmarshall/bwasw-nan
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Fail to infer insert size distribution when no pairs are within boundaries (re issue 108)
2017-07-30 16:53:04 -04:00
bcb475cd03
In bsw2_stat(), fail to infer when no pairs are within boundaries
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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
05c501332c
Merge branch 'dev'
2017-06-08 16:06:37 -04:00
298284d754
r1144: output debugging message to stderr
2017-06-08 16:06:13 -04:00
6442d009cd
updates grch38 URL
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simple URL update for grch38
fixes #111 , #115
grch37 link is still valid
2017-04-27 08:40:48 -04:00
9dfb9708db
Add -M option to bwakit
2016-11-09 11:36:55 -08:00
5961611c35
Merge branch 'dev'
2016-05-31 11:02:54 -04:00
f123871451
r1142: added option -5 for Hi-C data
2016-05-31 11:01:36 -04:00
08764215c6
Merge branch 'dev'
2016-05-31 09:43:16 -04:00
850dd811fc
Release bwa-0.7.15-r1140
2016-05-31 09:42:50 -04:00
bdfb9efaaa
Merge branch 'dev'
2016-05-20 18:06:03 -04:00
58bcc251f2
r1138: fixed typo in insert size estimate ( #65 )
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credit to @sjackman
2016-05-20 18:05:15 -04:00
ee730f3832
Merge branch 'dev'
2016-05-04 14:41:53 -04:00
5db0c362f5
Release 0.7.14-r1136
2016-05-04 14:41:37 -04:00
fe545f6ad5
Merge branch 'dev'
2016-05-03 11:29:43 -04:00
7ec3261877
r1134: use AH:* instead of AH:Y
2016-05-03 11:28:58 -04:00
6b9be61666
Merge branch 'master' of github.com:lh3/bwa
2016-04-28 15:40:57 -04:00
d668311f37
Merge branch 'dev'
2016-04-28 15:39:58 -04:00
3c038250f9
r1130: changed "ah" to "AH"
2016-04-28 15:39:18 -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
Heng Li
John Marshall
Brad Langhorst
Jacob Pfeil
Jason Gilliland
Steven Leonard
zengping