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  • 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
  • c6b226d719 r292: fixed a very stupid bug on CLI Heng Li 2013-02-26 12:49:48 -0500
  • bfb2583d7f r291: summary - bwt.c micro optimization Heng Li 2013-02-26 12:10:19 -0500
  • aa92c720b5 cleanup bwt_occ() Heng Li 2013-02-26 12:09:28 -0500
  • 80e1137a6c move bwt_invPsi() from bwt.h to bwt.c Heng Li 2013-02-26 11:57:36 -0500
  • fd67064207 removed an unnecessary condition Heng Li 2013-02-26 11:51:03 -0500
  • 264d5e42e5 simplified bwt_occ4() a little Heng Li 2013-02-26 11:49:39 -0500
  • c848b44481 code backup Heng Li 2013-02-26 11:22:24 -0500
  • 174fe0f1d5 code backup: less dependent on gcc optimization Heng Li 2013-02-26 11:14:19 -0500
  • e70c7c2a71 r284: amend cross-reference hit Heng Li 2013-02-26 00:03:49 -0500
  • 61dd3bf13a r283: prepare for fixing cross-ref aln Heng Li 2013-02-25 22:49:15 -0500
  • 77b5b586ad r282: set min split_len to read length Heng Li 2013-02-25 17:29:35 -0500
  • 30cc8a95d1 fixed an unimportant memory leak Heng Li 2013-02-25 16:34:19 -0500
  • d19e834d84 r280: align two ends in the same thread Heng Li 2013-02-25 15:40:15 -0500
  • 20aa848b3c r279: for PE mapq, consider the number of pairs Heng Li 2013-02-25 13:00:35 -0500
  • 9957e04590 r278: don't perform too many mate-sw Heng Li 2013-02-25 11:56:02 -0500
  • e9e5ee6a3d r277: updated the revision number Heng Li 2013-02-25 11:34:06 -0500
  • 5092211d75 controllable scoring matrix Heng Li 2013-02-25 11:24:21 -0500
  • 5ead86acd3 optionally mark split hit as secondary Heng Li 2013-02-25 11:18:35 -0500
  • 514563bd0a no poor hits with -a; reduce mapq for 2nd primary Heng Li 2013-02-25 10:54:12 -0500
  • 4dc982a3c7 support interleaved fastq Heng Li 2013-02-25 00:13:32 -0500
  • 570e082b38 change CC back to gcc Heng Li 2013-02-24 23:45:40 -0500
  • 29e41b592c bugfix: isize is off by 1 Heng Li 2013-02-24 23:00:51 -0500
  • 0b4a40dc25 updated revision number; to merge into master Heng Li 2013-02-24 13:34:20 -0500
  • 85775c3384 output multiple hits Heng Li 2013-02-24 13:23:43 -0500
  • 6bdccf2a8a added a bit documentation Heng Li 2013-02-24 13:09:29 -0500
  • ee59a13109 simplified bwamem.h Heng Li 2013-02-24 12:17:29 -0500
  • cda85be059 fixed a couple bugs identified by gcc Heng Li 2013-02-23 17:15:07 -0500
  • 6e7903e9f3 added kopen support Heng Li 2013-02-23 17:09:23 -0500