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938 Commits (7fe5a14058410f02dc7c05903da010580c96f2be)

Author SHA1 Message Date
Heng Li 05c501332c Merge branch 'dev' 2017-06-08 16:06:37 -04:00
Heng Li 298284d754 r1144: output debugging message to stderr 2017-06-08 16:06:13 -04:00
Ram Yalamanchili 7a77cc4785 Fix output file parameter for samtools sort 
samtools sort v0.7.15+ requires -o flag to specify the output file
 2017-05-18 15:42:25 -07:00
Gwen Ives 6a5caf764f Fixed BWTIncFree() memory leaks 
[Based on PR #37 with the additions below.]

Don't free non-malloced items in BWTFree().  If BWTCreate() is ever
called with a non-NULL decodeTable, BWTFree() will need to not free
decodeTable -- see FIXME comment.

Close packedFile in BWTIncConstructFromPacked() in the normal case.
Ignore it in error cases, as they immediately call exit() anyway.
 2017-05-12 16:34:57 +01:00
John Marshall 1972a97813 Only realloc(pac,...) if it needs to be made larger 
Similarly to the realloc(pac,...) within add1(), only bother to call
realloc() if appending the reverse complemented sequence requires more
space than is currently in the pac/m_pac buffer.

Avoids realloc(pac,0) (and a "Failed to allocate 0 bytes at bntseq.c"
message from wrap_realloc()) in the corner case of an empty reference
FASTA file.  Fixes #54.
 2017-05-10 19:47:12 +01:00
Brad Langhorst 6442d009cd updates grch38 URL 
simple URL update for grch38
fixes #111, #115
grch37 link is still valid
 2017-04-27 08:40:48 -04:00
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