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  • 0976272d99 Merge pull request #139 from jmarshall/fixes Heng Li 2017-07-30 18:36:07 -0400
  • a54e76945e Merge pull request #70 from rmzelle/patch-1 Heng Li 2017-07-30 17:01:27 -0400
  • 31bf49d814 Merge pull request #96 from jpfeil/master Heng Li 2017-07-30 16:57:30 -0400
  • 498973642f Merge pull request #123 from bwlang/patch-1 Heng Li 2017-07-30 16:55:39 -0400
  • 87ed015b24 Merge pull request #141 from jmarshall/bwasw-nan Heng Li 2017-07-30 16:53:04 -0400
  • c56c2e4677 Several trivial Debian patches Andreas Tille 2015-07-12 14:59:23 +0200
  • 3b96dcee7f Mem should set the mate cigar tag. Nils Homer 2017-06-25 08:02:42 -0700
  • bcb475cd03 In bsw2_stat(), fail to infer when no pairs are within boundaries John Marshall 2017-06-30 13:36:16 +0100
  • 690649872b Copy the whole kstring_t even if it contains NULs John Marshall 2017-06-30 12:46:56 +0100
  • a61b1dc610 Expand tot_seqs variable to long long John Marshall 2017-06-29 15:36:46 +0100
  • 5ede7eb981 Update README.md Rintze M. Zelle 2016-06-10 11:15:53 -0400
  • bc58bf265d Add "bwa mem -o FILE" synonym and documentation John Marshall 2017-06-27 17:05:44 +0100
  • d28da05f36 Added option to write output to file José Manuel Abuín Mosquera 2015-03-24 10:35:46 +0100
  • ab3a92bc73 Prevent Clang warnings on abs() and fabs() calls John Marshall 2017-06-26 10:45:13 +0100
  • 05c501332c Merge branch 'dev' Heng Li 2017-06-08 16:06:37 -0400
  • 298284d754 r1144: output debugging message to stderr Heng Li 2017-06-08 16:06:13 -0400
  • 7a77cc4785 Fix output file parameter for samtools sort Ram Yalamanchili 2017-05-18 15:23:05 -0700
  • 6a5caf764f Fixed BWTIncFree() memory leaks Gwen Ives 2014-12-09 10:24:46 +0100
  • 1972a97813 Only realloc(pac,...) if it needs to be made larger John Marshall 2017-05-10 19:47:12 +0100
  • 6442d009cd updates grch38 URL Brad Langhorst 2017-04-27 08:40:48 -0400
  • beff2e27f8 Add missing <stdint.h> include John Marshall 2017-04-25 13:54:31 +0100
  • af87825525 Replace u_int32_t by the more common uint32_t John Marshall 2017-04-25 13:51:52 +0100
  • 9dfb9708db Add -M option to bwakit Jacob Pfeil 2016-11-07 16:52:54 -0800
  • 8cc02badd9 Forbid literal TAB control characters in @RG line James Blachly 2016-08-09 17:05:51 -0400
  • 00e59ddbae Update README.md Rintze M. Zelle 2016-06-10 11:15:53 -0400
  • 5961611c35 Merge branch 'dev' Heng Li 2016-05-31 11:02:54 -0400
  • f123871451 r1142: added option -5 for Hi-C data Heng Li 2016-05-31 11:01:36 -0400
  • 08764215c6 Merge branch 'dev' Heng Li 2016-05-31 09:43:16 -0400
  • 850dd811fc Release bwa-0.7.15-r1140 Heng Li 2016-05-31 09:42:50 -0400
  • bdfb9efaaa Merge branch 'dev' Heng Li 2016-05-20 18:06:03 -0400
  • 58bcc251f2 r1138: fixed typo in insert size estimate (#65) Heng Li 2016-05-20 18:05:15 -0400
  • ee730f3832 Merge branch 'dev' Heng Li 2016-05-04 14:41:53 -0400
  • 5db0c362f5 Release 0.7.14-r1136 Heng Li 2016-05-04 14:41:37 -0400
  • fe545f6ad5 Merge branch 'dev' Heng Li 2016-05-03 11:29:43 -0400
  • 7ec3261877 r1134: use AH:* instead of AH:Y Heng Li 2016-05-03 11:28:58 -0400
  • 6b9be61666 Merge branch 'master' of github.com:lh3/bwa Heng Li 2016-04-28 15:40:57 -0400
  • d668311f37 Merge branch 'dev' Heng Li 2016-04-28 15:39:58 -0400
  • 3c038250f9 r1130: changed "ah" to "AH" Heng Li 2016-04-28 15:39:18 -0400
  • d6636daead Include in man page info on read types Jason Gilliland 2016-03-31 12:39:24 -0400
  • e10fc577e1 Fix a few typos in man page Jason Gilliland 2016-03-31 12:26:42 -0400
  • bb7533e32c Merge pull request #55 from jdagilliland/master Heng Li 2016-03-17 12:15:12 -0400
  • 6460ef5572 Minor doc fix Jason Gilliland 2016-03-17 11:50:00 -0400
  • 2c078eb667 option to skip ALT Heng Li 2016-03-16 16:06:49 -0400
  • 83662032a2 Merge branch 'dev' Heng Li 2016-02-23 11:24:40 -0500
  • 9e5852c540 Released bwa-0.7.13 (r1126) Heng Li 2016-02-23 11:24:19 -0500
  • 67aa1ca731 Merge branch 'dev' Heng Li 2016-02-23 11:17:21 -0500
  • b94a78adbf use /usr/env/perl Heng Li 2016-02-23 11:08:43 -0500
  • f1ce529cd9 added comment Heng Li 2016-02-23 11:08:11 -0500
  • 11437a14f4 Port #48 to the dev branch Heng Li 2016-02-23 11:07:27 -0500
  • 5ecdc66e46 Merge branch 'master' of github.com:lh3/bwa Heng Li 2016-02-23 11:05:47 -0500
  • f9a7869079 Merge pull request #48 from srl147/master Heng Li 2016-02-23 11:05:35 -0500
  • 4820d8fc32 Merge branch 'dev' Heng Li 2016-02-23 10:40:26 -0500
  • 9a828344ec moved indexing to libbwa Heng Li 2016-02-13 18:48:46 -0500
  • 099c24f5fc fix assertion failure report on bio-bwa-help mailing list bwase.c:180: bwa_refine_gapped_core: Assertion `re - rb == rlen' failed Steven Leonard 2016-02-11 14:00:18 +0000
  • cc9eef2d33 Merge branch 'dev' Heng Li 2016-02-01 11:57:56 -0500
  • 86170ffd2f r1102: resumed versioning Heng Li 2016-02-01 11:57:14 -0500
  • 25097a9a88 Merge branch 'dev' Heng Li 2016-02-01 11:52:02 -0500
  • ede7b092a2 updated GRCh38 download link Heng Li 2016-02-01 11:50:25 -0500
  • 1e6a10ce2d a typo in fastmap command-line prompt Heng Li 2016-02-01 11:41:46 -0500
  • 6f0ea0b7e3 use /usr/bin/env perl Heng Li 2016-02-01 11:39:50 -0500
  • fdf47000e7 integer overflow on indexing Heng Li 2016-01-26 23:21:23 -0500
  • c819643412 make kthread.c compiled with g++ Heng Li 2016-01-26 22:49:28 -0500
  • 1247dc2346 removed the pbread mode Heng Li 2016-01-26 22:37:01 -0500
  • 616a53491d Merge branch 'dev' of github.com:lh3/bwa into dev Heng Li 2016-01-26 17:19:16 -0500
  • feeb41f42d updated dependencies Heng Li 2016-01-26 13:54:47 -0500
  • be2020c4af ropebwt2 for bwt construction Heng Li 2016-01-26 13:46:08 -0500
  • 1b2e9a6d89 Merge pull request #51 from sethbrin/master Heng Li 2016-01-21 14:10:32 -0500
  • 1ec736e06a Merge pull request #50 from mgymrek/patch-1 Heng Li 2016-01-20 09:58:59 -0500
  • 176a7ec67e update the usage of main_fastmap zengping 2016-01-20 22:52:25 +0800
  • 9be943cec0 Editing URL for b38 download Melissa Gymrek 2016-01-17 10:58:02 -0500
  • f9ce2a6c73 fix a bug where bwa_sa2pos could return without setting strand Steven Leonard 2015-12-11 09:29:27 +0000
  • e3ea2a8222 Merge pull request #47 from mfcovington/feature/fix-maxk-error Heng Li 2015-11-14 20:47:22 -0500
  • c2efebefa7 Include 'unistd.h' to explicitly declare 'getopt' Mike Covington 2015-11-14 17:27:57 -0800
  • 0911122749 Merge branch 'master' of github.com:lh3/bwa Heng Li 2015-08-27 10:44:55 -0400
  • e8d531189f Merge branch 'dev' Heng Li 2015-08-27 10:44:34 -0400
  • 6c668d3e1a fixed a bug in reverse-complement Heng Li 2015-08-27 10:44:08 -0400
  • 9812521922 Merge pull request #43 from wookietreiber/perl-shebangs Heng Li 2015-07-02 11:52:40 -0400
  • b1a96f58b6 use more portable /usr/bin/env perl for scripts Christian Krause 2015-07-02 15:23:40 +0200
  • eb428d7d31 Merge branch 'dev' Heng Li 2015-03-25 12:18:22 -0400
  • 3ae437ac13 r1044: fixed an out-of-order bug in kthread Heng Li 2015-03-25 12:16:06 -0400
  • 163f949a33 added maxk: max unique k-mer at each position Heng Li 2015-02-08 16:49:25 -0500
  • 1e29bccc65 Merge branch 'dev' Heng Li 2014-12-29 16:43:42 -0500
  • 1f99921b73 changed download link: 0.7.11 => 0.7.12 Heng Li 2014-12-29 16:43:22 -0500
  • 5a340797e7 Merge branch 'dev' Heng Li 2014-12-28 15:45:11 -0500
  • 8211fbcb62 Released 0.7.12 Heng Li 2014-12-28 15:44:59 -0500
  • e746a3eac7 r1038: wrong 0x100|0x800 flags in PE mode Heng Li 2014-12-24 13:22:46 -0500
  • 3ae8d4b80b r1037: wrong read number flag Heng Li 2014-12-24 00:55:33 -0500
  • b9bbf2d3df r1036: PE ALT mapping incorrect Heng Li 2014-12-24 00:49:50 -0500
  • b8e189c1e5 Merge branch 'dev' Heng Li 2014-12-23 15:29:34 -0500
  • 408fd5e072 Released bwa-0.7.11-r1034 Heng Li 2014-12-23 15:29:18 -0500
  • d7ce7e1395 hs38D1=>hs38DH; cmd help for run-gen-ref Heng Li 2014-12-23 11:48:59 -0500
  • ed95769a33 updated documentations Heng Li 2014-12-21 16:30:29 -0500
  • c05a721f28 improved doc and don't type HLA by default Heng Li 2014-12-21 00:12:11 -0500
  • 5aba188969 write empty .gt file as a placeholder Heng Li 2014-12-20 22:27:27 -0500
  • 32c4e3fe5a updated decoy sequences and names Heng Li 2014-12-20 22:24:13 -0500
  • 4ffdc7b5ad Merge branch 'dev' Heng Li 2014-12-19 07:50:23 -0500
  • c561759222 r1027: segfault caused by the last commit Heng Li 2014-12-12 16:56:54 -0500
  • 4e705c037e Merge branch 'dev' Heng Li 2014-12-11 10:39:04 -0500
  • 925ddfb697 r1025: accept file with -H; allow to replace @SQ Heng Li 2014-12-11 10:38:36 -0500
  • 139df93af9 Merge branch 'dev' Heng Li 2014-12-10 23:21:13 -0500