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  • db7a98636f r380: er... another compiling error Heng Li 2013-04-19 12:04:44 -0400
  • f0c94d80d1 r379: fixed compiling error Heng Li 2013-04-19 12:04:00 -0400
  • be11e27e12 r378: bugfix - wrong CIGAR Heng Li 2013-04-19 12:00:37 -0400
  • 2087dc162f r377: increased unpaired penalty from 9 to 17 Heng Li 2013-04-17 16:50:20 -0400
  • 3dd10bd7db Merge branch 'master' into master_fixes Rob Davies 2013-04-12 16:20:13 +0100
  • 90ecd344ba Merge branch 'master' into master_fixes. Merged up to master r375. Rob Davies 2013-04-11 11:15:39 +0100
  • 499cf4c00d r376: reduce wasteful seed extension Heng Li 2013-04-10 12:18:56 -0400
  • 47520134e7 r375: fixed compiling errors by the last change Heng Li 2013-04-10 11:04:32 -0400
  • 3d8a8c1e37 r374: fix - clipping penalty not always working Heng Li 2013-04-10 01:09:37 -0400
  • 53bb846407 r373: optionally distable mate rescue Heng Li 2013-04-09 16:13:55 -0400
  • d64eaa851d fixed an issue caused by a Mac/Darwin bug Heng Li 2013-04-09 15:17:04 -0400
  • d7ca0885eb r371: extend overlapping seeds Heng Li 2013-04-04 00:43:43 -0400
  • 1e118e0823 r370: suppress "D" at the end of a cigar Heng Li 2013-04-03 23:57:19 -0400
  • c89756e2b0 Merge branch 'master' into master_fixes Rob Davies 2013-03-19 12:11:51 +0000
  • 8437cd4edd r369: bugfix - segfault caused by the last change Heng Li 2013-03-19 01:04:57 -0400
  • 1e3cadbfc2 r368: bugfix - wrong CIGAR when bridging 3 contigs Heng Li 2013-03-18 20:49:32 -0400
  • c862a1a396 Merge branch 'master' into master_fixes Rob Davies 2013-03-18 13:35:12 +0000
  • 9346acde1b Release bwa-0.7.3a-r367 Heng Li 2013-03-15 21:26:37 -0400
  • 7dec00c217 Release BWA-0.7.3-r366 Heng Li 2013-03-15 12:51:53 -0400
  • dd51177837 r365: bugfix - wrong alignment (right mapping) Heng Li 2013-03-15 11:59:05 -0400
  • e5355fe3a0 r364: bug in mem pairing (no effect with -A=1) Heng Li 2013-03-14 22:01:26 -0400
  • cca27c1ef5 Merge branch 'master' into master_fixes Rob Davies 2013-03-13 12:12:28 +0000
  • 925aa6f60d Added Makefile.bak and bwamem-lite to .gitignore Rob Davies 2013-03-13 09:18:18 +0000
  • bdf34f6ce7 r363: XA=>XP; output mapQ in XP Heng Li 2013-03-12 09:56:04 -0400
  • c29b176cb6 r362: bugfix - occasionally wrong TLEN Heng Li 2013-03-12 00:14:36 -0400
  • aa7cdf4bb3 r361: flag proper pair even if multi-primary Heng Li 2013-03-12 00:00:04 -0400
  • dab5b17c1a r360: output alternative primary alignments in XA Heng Li 2013-03-11 23:43:58 -0400
  • 6c665189ad r359: identical output to 0.7.2 (without -a) Heng Li 2013-03-11 23:16:18 -0400
  • 0f88103d2a SAM almost identical to 0.7.2 Heng Li 2013-03-11 23:01:51 -0400
  • 26f4c704ed drop the old SAM writer Heng Li 2013-03-11 22:24:54 -0400
  • 0b0455ca51 replace PE; BUGGY right now!! Heng Li 2013-03-11 22:18:23 -0400
  • ebb45dc42e new code works for SE Heng Li 2013-03-11 21:59:15 -0400
  • c7edaa8e84 to test the new sam writer... Heng Li 2013-03-11 21:55:52 -0400
  • 47952b6f3f drop an unnecessary member from mem_aln_t Heng Li 2013-03-11 21:35:32 -0400
  • 8f0d439913 prepare to replace the SAM printing code Heng Li 2013-03-11 21:25:17 -0400
  • 9228e48efd Merge branch 'master' into master_fixes Rob Davies 2013-03-11 13:50:49 +0000
  • 5581cb9152 Release bwa-0.7.2-r351 Heng Li 2013-03-09 18:15:41 -0500
  • 2d01a297fb Improving 'properly paired' flag. Heng Li 2013-03-09 18:05:50 -0500
  • 740d2c1314 Match to 'N' costs -1, instead of 0. Heng Li 2013-03-09 18:03:57 -0500
  • 9ea7f83974 Emergent bugfix: wrong TLEN sign Heng Li 2013-03-09 18:03:15 -0500
  • 1d132a546d Release 0.7.1-r347 Heng Li 2013-03-08 15:30:06 -0500
  • 5370bb23a3 Updated NEWS; added stddef.h for size_t Heng Li 2013-03-08 14:14:42 -0500
  • 66c9783daf r345: bugfix in mem - wrong mate strand for unmap Heng Li 2013-03-08 13:15:43 -0500
  • af7b4d8980 gcc wrongly thinks a variable may be uninitialized Heng Li 2013-03-08 12:45:50 -0500
  • 274c0ac96c r343: bugfix in mem - wrong mate info for unmap Heng Li 2013-03-08 12:40:31 -0500
  • 017be45407 r342: bugfix in bwasw - AS is off by one Heng Li 2013-03-08 12:06:45 -0500
  • aabd990e8f Merge branch 'master' into master_fixes Rob Davies 2013-03-08 16:46:45 +0000
  • b5b50ac8da r341: bugfix - wrong mate position Heng Li 2013-03-07 21:35:57 -0500
  • b0a76884e8 r340: feature freeze; updated the manpage Heng Li 2013-03-07 11:51:23 -0500
  • 503ca9ed2e r339: pemerge - expose some settings to CLI Heng Li 2013-03-07 11:22:19 -0500
  • 1cadfa1552 r338: pemerge - fixed memory leaks; multithreading Heng Li 2013-03-07 11:14:52 -0500
  • 3e3236dfc4 r337: mem - always read even number of reads Heng Li 2013-03-07 11:00:15 -0500
  • 72817b664e r336: fine tuning pemerge Heng Li 2013-03-06 23:38:07 -0500
  • 557d50c7e1 r335: fixed a compiling error Heng Li 2013-03-06 21:57:13 -0500
  • 042e1f4442 r334: added pemerge to bwa Heng Li 2013-03-06 21:55:02 -0500
  • 773b86331b De-overlap paired-end reads Heng Li 2013-03-06 19:23:45 -0500
  • 5fbd454682 r332: added output threshold Heng Li 2013-03-05 22:49:38 -0500
  • 6476343a83 r331: rewrote CIGAR generation for bwa-short Heng Li 2013-03-05 19:56:37 -0500
  • a76b75f41e Merge pull request #14 from drkeoni/master Heng Li 2013-03-05 12:57:10 -0800
  • 25366c7220 Fixing problem with linking to libm on some Ubuntu systems (I see this on machine running 11.04, kernel 3.0.0-14-virtual). Changing order of -lm on the command line seems to do the trick and should be tolerated in other environments. Jon Sorenson 2013-03-05 20:48:16 +0000
  • 98f8966750 r329: ditch stdaln.{c,h}; no changes to bwa-mem Heng Li 2013-03-05 12:00:24 -0500
  • bb37e14d02 replace aln_global in bwase.c Heng Li 2013-03-05 10:38:47 -0500
  • e6c262594f bwa-sw: ditch stdaln Heng Li 2013-03-05 10:12:38 -0500
  • 086c9d0e7d bwa-sw: use bwa_gen_cigar() for cigar generation Heng Li 2013-03-05 09:54:49 -0500
  • 07921659cf move mem_fill_scmat() to bwa.{h,c} Heng Li 2013-03-05 09:38:12 -0500
  • 8a078cc16d Merge branch 'master' into master_fixes Rob Davies 2013-03-05 10:21:07 +0000
  • efd9769b07 r324: a little code cleanup Heng Li 2013-03-05 00:57:16 -0500
  • e0991d6a45 r323: added Z-dropoff, a variant of blast's X-drop Heng Li 2013-03-05 00:34:33 -0500
  • d6096c3f99 bugfix: caused by the latest change Heng Li 2013-03-04 18:41:57 -0500
  • 59bc9341f6 code backup; more changes coming later Heng Li 2013-03-04 17:29:07 -0500
  • 733410b50d r320: speed up very long sequence alignment Heng Li 2013-03-04 14:43:49 -0500
  • 40f1214736 change to debugging code only Heng Li 2013-03-04 11:52:11 -0500
  • 7e00dbcac5 r317: bugfix - out-of-range extension Heng Li 2013-03-04 11:35:23 -0500
  • 1a451df800 prepare to ditch stdaln.{h,c} Heng Li 2013-03-04 10:32:33 -0500
  • d35f33b513 r316: don't allocate zero-length memory Heng Li 2013-03-04 10:22:18 -0500
  • 35fb7f9fdf r315: move kopen.o out of libbwa.a Heng Li 2013-03-01 11:47:51 -0500
  • 3e4a178e08 r314: cleanup bwamem API Heng Li 2013-03-01 11:14:51 -0500
  • 6beab5f765 Merge branch 'master' into master_fixes Rob Davies 2013-03-01 10:22:49 +0000
  • 3d33ab063e Merge branch 'master' into master_fixes Rob Davies 2013-03-01 09:37:46 +0000
  • c5434ac865 r313: release bwa-0.7.0 Heng Li 2013-02-28 15:56:05 -0500
  • 39fcde9c19 updated NEWS further Heng Li 2013-02-28 00:58:24 -0500
  • f3cff1c609 r311: even tighter bw for CIGAR Heng Li 2013-02-27 23:59:50 -0500
  • a33b9c0633 tighter bw for cigar SW Heng Li 2013-02-27 23:40:46 -0500
  • 6a4d8c79d8 r309: bugfix - soft clipping missing in example.c Heng Li 2013-02-27 22:45:18 -0500
  • df7c3f0000 r308: added a new API to convert region to CIGAR Heng Li 2013-02-27 22:28:29 -0500
  • 64d92d26df more documentation in ksw.h Heng Li 2013-02-27 21:40:46 -0500
  • 4bb0bdddca r306: introduce clipping penalty Heng Li 2013-02-27 21:13:39 -0500
  • b7791105bc r305: in NEWS, convert TAB to space Heng Li 2013-02-27 16:56:54 -0500
  • aef179a580 r304: prepare release notes (not released yet) Heng Li 2013-02-27 16:55:07 -0500
  • 292e92b602 r303: bugfix - wrong band width when CIGAR Heng Li 2013-02-27 15:39:15 -0500
  • e620f0ff4e r302: updated the manpage Heng Li 2013-02-27 13:16:22 -0500
  • b621d3ae38 r301: left-align indels Heng Li 2013-02-27 00:42:19 -0500
  • 65e099df34 r300: fixed an out-of-boundary bug in rare case Heng Li 2013-02-27 00:37:17 -0500
  • 0b533385ef r299: better way to exclude seed Heng Li 2013-02-27 00:29:11 -0500
  • ee80fb8bd0 Test each seed to see if extension is needed Heng Li 2013-02-26 22:55:44 -0500
  • acd1ab607b r297: reduce wasteful SW extension Heng Li 2013-02-26 16:26:46 -0500
  • 54ab3bbec7 Dropped solid2fastq.pl Heng Li 2013-02-26 14:35:03 -0500
  • 98787f0ae0 r295: generate NM Heng Li 2013-02-26 13:36:01 -0500
  • 32f2d60a2e r294: bugfix - -M not working Heng Li 2013-02-26 13:14:33 -0500
  • 619ac4f93d r293: bugfix - wrong RG type in SAM output Heng Li 2013-02-26 13:03:35 -0500