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  • 2e9463ebf1 dev-r442: suppress exact full-length matches Heng Li 2014-02-26 22:04:19 -0500
  • 1c19bc630f Released bwa-0.7.7-r441 Heng Li 2014-02-25 01:05:37 -0500
  • e879817373 r440: a condition not work due to a typo Heng Li 2014-02-20 13:06:40 -0500
  • ce026a07fc r439: expose mem_opt_t::max_matesw Heng Li 2014-02-19 13:10:33 -0500
  • 17fb85a227 r438: still an issue in MD Heng Li 2014-02-19 11:31:54 -0500
  • 52391a9855 r437: print timing for each batch of reads Heng Li 2014-02-19 10:54:26 -0500
  • bdd14d2946 r436: fix rare MD/NM-CIGAR inconsistencies Heng Li 2014-02-19 10:08:43 -0500
  • 4adc34eccb r435: bugfix - base not complemented on the rev Heng Li 2014-02-18 10:32:24 -0500
  • 14aa43cca0 r434: added the missing bwasw/aln commands! Heng Li 2014-02-12 15:39:02 -0500
  • 7c50bad567 Release bwa-0.7.6a-r433 Heng Li 2014-01-31 12:58:21 -0500
  • 5fdab3ae13 Released bwa-0.7.6-r432 Heng Li 2014-01-31 11:12:59 -0500
  • f524c7d3d8 r431: added the MD tag to bwa-mem Heng Li 2014-01-29 12:05:11 -0500
  • ea3dc2f003 r430: fix a bug producing incorrect alignment Heng Li 2014-01-29 10:51:02 -0500
  • d17ae1e808 Merge pull request #21 from bpow/fix-duplicate-pg Heng Li 2014-01-06 06:41:16 -0800
  • c26ba4e376 fix duplicate PG lines in bwape and bwase Bradford Powell 2014-01-05 14:54:48 -0500
  • 10cb6b0507 r428: allow to change the default chain_drop_ratio Heng Li 2013-12-30 16:18:45 -0500
  • 3afcdc7746 debugging code only: print seeds Heng Li 2013-12-30 16:05:43 -0500
  • 74a1a53499 print debugging msg to stdout Heng Li 2013-12-30 15:49:41 -0500
  • f70d80a5a2 r427: fixed bugs in backtrack Heng Li 2013-12-30 15:40:18 -0500
  • 8b6ec74907 r424: fixed a bw bug in samse/pe Heng Li 2013-11-25 15:48:04 -0500
  • 4219e58623 r423: bugfix - SE hits not random Heng Li 2013-11-23 09:36:26 -0500
  • 29aa855432 r422: matesw hits not sorted Heng Li 2013-11-21 14:43:50 -0500
  • ff4762f3c7 r421: bw doubling in the final alignment Heng Li 2013-11-20 10:04:16 -0500
  • 6e3fa0515a r420: inferred bandwidth is not used in the final Heng Li 2013-11-20 09:50:46 -0500
  • ff6faf811a r419: print the @PG line Heng Li 2013-11-19 11:08:45 -0500
  • deb19593aa r418: use the new mapQ estimator by default Heng Li 2013-11-02 12:25:53 -0400
  • 19d33faa30 use kthread for multi-threading Heng Li 2013-11-02 12:13:11 -0400
  • c564653b40 r416: removed a line of debugging code Heng Li 2013-09-12 10:41:43 -0400
  • 7144a0cefc r415: bug in the new (optional) mapQ computation Heng Li 2013-09-09 17:51:05 -0400
  • ebb7b02e9b r414: fixed a bug caused by the last commit Heng Li 2013-09-09 16:57:55 -0400
  • b51a66e4c1 r413: fixed an issue causing redundant alignment Heng Li 2013-09-09 11:36:50 -0400
  • 1e2cff20ba more conservative mapQ Heng Li 2013-09-09 08:57:45 -0400
  • 1346f03ff1 use the old mapQ by default Heng Li 2013-09-06 14:04:41 -0400
  • 451d60f3be slight modification Heng Li 2013-09-06 12:37:38 -0400
  • 623da055e1 alternative way to estimate mapQ Heng Li 2013-09-06 12:31:47 -0400
  • ed78df9184 Merge branch 'master' into clip2 Heng Li 2013-08-28 16:00:34 -0400
  • 3b84c03c1e r406: allow to use diff clipping penalties Heng Li 2013-08-28 15:59:05 -0400
  • 426e54740c Merge pull request #19 from jmarshall/check-qnames Heng Li 2013-06-14 06:27:41 -0700
  • b88718d8f4 Reformat note for 80 columns, and fix typo John Marshall 2013-06-14 14:03:08 +0100
  • 128ffc089b Complain when bwa mem is given too many filenames John Marshall 2013-06-14 14:00:24 +0100
  • 20dc9dd41a Check that paired reads have the same QNAME John Marshall 2013-06-14 13:57:22 +0100
  • 7ec8b5c9e7 Release bwa-0.7.5a Heng Li 2013-05-30 16:20:16 -0400
  • ef18cb91cb Release bwa-0.7.5-r404 Heng Li 2013-05-29 11:49:08 -0400
  • 01c9cd152b fixed a typo in NEWS Heng Li 2013-05-28 13:40:31 -0400
  • 4e992769d5 r402: updated NEWS (prepare for the 0.7.5 release) Heng Li 2013-05-28 11:18:42 -0400
  • 73619754f8 r401: bugfix - forgot to change sampe Heng Li 2013-05-27 22:24:35 -0400
  • 6fed8fa0b4 minor changes Heng Li 2013-05-24 21:17:49 -0400
  • 02d9bf123f Minor formatting issues Heng Li 2013-05-24 20:51:24 -0400
  • 607e11d43d updated README Heng Li 2013-05-24 20:49:36 -0400
  • 599e840779 r397: multi changes/bugfixes to bwa-backtrack Heng Li 2013-05-24 16:28:18 -0400
  • bde5005f39 r396: er... the new tag is named SA not SP Heng Li 2013-05-23 12:48:18 -0400
  • 3d2450ed97 r395: bugfix - hard clipping not applied on revaln Heng Li 2013-05-23 12:45:14 -0400
  • 9441bb7f2a r394: added future plan Heng Li 2013-05-22 20:02:53 -0400
  • 0e759bc1f5 removed a redundant flag Heng Li 2013-05-22 19:55:07 -0400
  • 9735d7a31a conform to the latest (unpublished) SAM spec Heng Li 2013-05-22 19:45:16 -0400
  • 9a6abe51b6 r391: better method to resolve xref alignment Heng Li 2013-05-22 18:57:51 -0400
  • 338ebfaae0 Merge pull request #13 from daviesrob/master_fixes Heng Li 2013-05-03 05:07:47 -0700
  • 5c43a1fdc9 Removed more dependencies on utils.h Rob Davies 2013-05-03 11:38:48 +0100
  • 96e445d9e4 Reduce dependency on utils.h - new malloc wrapping scheme. Rob Davies 2013-05-02 15:12:01 +0100
  • 0aa7e0a402 Ensure exit status of 1 if given invalid options or index files are not found. Rob Davies 2013-04-29 13:58:28 +0100
  • e88529687f Merge branch 'master' into master_fixes. Merged up to r389. Rob Davies 2013-04-29 12:09:30 +0100
  • 1a2bd2cf91 r389: return non-zero upon errors Heng Li 2013-04-27 10:08:01 -0400
  • 19cb7cd7ed r388: cleanup mem_process_seqs() interface Heng Li 2013-04-26 12:31:18 -0400
  • 8896cb942e r386: bugfix - samse/pe segfault Heng Li 2013-04-24 16:00:02 -0400
  • b3d0a13b32 Merge branch 'master' into master_fixes. Merged up to release bwa-0.7.4-r385. Rob Davies 2013-04-23 17:31:34 +0100
  • 6b59bc5500 r386: typo in NEWS Heng Li 2013-04-23 12:30:22 -0400
  • c14aaad1ce Released bwa-0.7.4-r385 Heng Li 2013-04-23 11:40:56 -0400
  • 2f6897c72b r384: don't compile bwamem-lite by default Heng Li 2013-04-23 11:27:30 -0400
  • 78ed00021f r384: updated NEWS Heng Li 2013-04-23 11:25:46 -0400
  • 4cb5110d03 Merge branch 'master' into master_fixes Rob Davies 2013-04-22 09:51:07 +0100
  • f6ae0d4d0f r382: similar treatment in bwa-sw (see r381) Heng Li 2013-04-19 17:52:06 -0400
  • 3f8caef33c r381: fixed a bug when upper bound < max read len Heng Li 2013-04-19 17:44:35 -0400
  • 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