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932 Commits (f717ea131837acd8cf85eaffb0e3584794f853a7)

Author SHA1 Message Date
John Marshall beff2e27f8 Add missing <stdint.h> include 
Fixes compilation on non-glibc platforms, e.g., FreeBSD and Alpine Linux.
 2017-04-25 13:54:31 +01:00
John Marshall af87825525 Replace u_int32_t by the more common uint32_t 
The u_int32_t type comes from <sys/types.h>, which is often included
as a byproduct of other headers on glibc platforms, but not on FreeBSD
or Alpine Linux.  Use <stdint.h>'s uint32_t instead, which is used
elsewhere in bwa source code.
 2017-04-25 13:51:52 +01:00
Jacob Pfeil 9dfb9708db Add -M option to bwakit 2016-11-09 11:36:55 -08:00
James Blachly 8cc02badd9 Forbid literal TAB control characters in @RG line 2016-08-09 17:05:51 -04:00
Rintze M. Zelle 00e59ddbae Update README.md 
Correct header formatting, fix some typos in headers
 2016-06-10 11:15:53 -04:00
Heng Li 5961611c35 Merge branch 'dev' 2016-05-31 11:02:54 -04:00
Heng Li f123871451 r1142: added option -5 for Hi-C data 2016-05-31 11:01:36 -04:00
Heng Li 08764215c6 Merge branch 'dev' 2016-05-31 09:43:16 -04:00
Heng Li 850dd811fc Release bwa-0.7.15-r1140 2016-05-31 09:42:50 -04:00
Heng Li bdfb9efaaa Merge branch 'dev' 2016-05-20 18:06:03 -04:00
Heng Li 58bcc251f2 r1138: fixed typo in insert size estimate (#65) 
credit to @sjackman
 2016-05-20 18:05:15 -04:00
Heng Li ee730f3832 Merge branch 'dev' 2016-05-04 14:41:53 -04:00
Heng Li 5db0c362f5 Release 0.7.14-r1136 2016-05-04 14:41:37 -04:00
Heng Li fe545f6ad5 Merge branch 'dev' 2016-05-03 11:29:43 -04:00
Heng Li 7ec3261877 r1134: use AH:* instead of AH:Y 2016-05-03 11:28:58 -04:00
Heng Li 6b9be61666 Merge branch 'master' of github.com:lh3/bwa 2016-04-28 15:40:57 -04:00
Heng Li d668311f37 Merge branch 'dev' 2016-04-28 15:39:58 -04:00
Heng Li 3c038250f9 r1130: changed "ah" to "AH" 2016-04-28 15:39:18 -04:00
Jason Gilliland d6636daead Include in man page info on read types 
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
Jason Gilliland e10fc577e1 Fix a few typos in man page 2016-03-31 12:40:03 -04:00
Heng Li bb7533e32c Merge pull request #55 from jdagilliland/master 
Minor doc fix
 2016-03-17 12:15:12 -04:00
Jason Gilliland 6460ef5572 Minor doc fix 
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
Heng Li 2c078eb667 option to skip ALT 2016-03-16 16:06:49 -04:00
Heng Li 83662032a2 Merge branch 'dev' 2016-02-23 11:24:40 -05:00
Heng Li 9e5852c540 Released bwa-0.7.13 (r1126) 2016-02-23 11:24:19 -05:00
Heng Li 67aa1ca731 Merge branch 'dev' 2016-02-23 11:17:21 -05:00
Heng Li b94a78adbf use /usr/env/perl 2016-02-23 11:08:43 -05:00
Heng Li f1ce529cd9 added comment 2016-02-23 11:08:11 -05:00
Heng Li 11437a14f4 Port #48 to the dev branch 2016-02-23 11:07:27 -05:00
Heng Li 5ecdc66e46 Merge branch 'master' of github.com:lh3/bwa 2016-02-23 11:05:47 -05:00
Heng Li f9a7869079 Merge pull request #48 from srl147/master 
ensure bwa_sa2pos does not return without setting strand
 2016-02-23 11:05:35 -05:00
Heng Li 4820d8fc32 Merge branch 'dev' 2016-02-23 10:40:26 -05:00
Heng Li 9a828344ec moved indexing to libbwa 2016-02-13 18:48:46 -05:00
Steven Leonard 099c24f5fc fix assertion failure report on bio-bwa-help mailing list 
bwase.c:180: bwa_refine_gapped_core: Assertion `re - rb == rlen' failed
 2016-02-11 14:00:18 +00:00
Heng Li cc9eef2d33 Merge branch 'dev' 2016-02-01 11:57:56 -05:00
Heng Li 86170ffd2f r1102: resumed versioning 2016-02-01 11:57:14 -05:00
Heng Li 25097a9a88 Merge branch 'dev' 2016-02-01 11:52:02 -05:00
Heng Li ede7b092a2 updated GRCh38 download link 2016-02-01 11:50:25 -05:00
Heng Li 1e6a10ce2d a typo in fastmap command-line prompt 2016-02-01 11:41:46 -05:00
Heng Li 6f0ea0b7e3 use /usr/bin/env perl 2016-02-01 11:39:50 -05:00
Heng Li fdf47000e7 integer overflow on indexing 2016-01-26 23:21:23 -05:00
Heng Li c819643412 make kthread.c compiled with g++ 2016-01-26 22:49:28 -05:00
Heng Li 1247dc2346 removed the pbread mode 
It is not working well. Not at all.
 2016-01-26 22:37:01 -05:00
Heng Li 616a53491d Merge branch 'dev' of github.com:lh3/bwa into dev 2016-01-26 17:19:16 -05:00
Heng Li feeb41f42d updated dependencies 2016-01-26 13:54:47 -05:00
Heng Li be2020c4af ropebwt2 for bwt construction 2016-01-26 13:46:08 -05:00
Heng Li 1b2e9a6d89 Merge pull request #51 from sethbrin/master 
update the usage of main_fastmap
 2016-01-21 14:10:32 -05:00
Heng Li 1ec736e06a Merge pull request #50 from mgymrek/patch-1 
Editing URL for b38 download
 2016-01-20 09:58:59 -05:00
zengping 176a7ec67e update the usage of main_fastmap 2016-01-20 22:52:25 +08:00
Melissa Gymrek 9be943cec0 Editing URL for b38 download 
The previous link appears to no longer exist.
 2016-01-17 10:58:02 -05:00