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  • 8220008564 an attempt to layout tool Heng Li 2014-04-09 16:11:52 -0400
  • db58392e9b dev-469: fixed wrong command line prompt Heng Li 2014-04-09 13:20:04 -0400
  • d766591c1e dev-468: fixed a segfault caused by NULL Heng Li 2014-04-08 22:11:36 -0400
  • 99f6f9a0d1 dev-467: limit the max #chains to extend Heng Li 2014-04-08 21:45:49 -0400
  • c0a308a8b6 dev-466: simplified chain filtering Heng Li 2014-04-08 17:33:07 -0400
  • f12dfae772 dev-465: a new output format for read overlap Heng Li 2014-04-08 16:29:36 -0400
  • b45aeb87e1 dev-464: preset for pacbio read2read aln Heng Li 2014-04-08 11:40:54 -0400
  • 172ba83241 dev-463: added option -x to change multiple params Heng Li 2014-04-07 11:29:36 -0400
  • 114901b005 dev-r462: refined setting for PacBio; weight flt Heng Li 2014-04-04 17:01:04 -0400
  • 41f720dfa7 dev-461: added a heuristic for PacBio data Heng Li 2014-04-04 16:05:41 -0400
  • 066ec4aa95 dev-460: disallow a cigar 20M2D2I30M in extension Heng Li 2014-04-04 10:44:34 -0400
  • b6bd33b26c dev-459: don't hard code the drop ratio Heng Li 2014-04-03 18:58:49 -0400
  • b3225581be dev-458: simplified the smem iterator Heng Li 2014-04-03 15:23:48 -0400
  • acfe7613db dev-457: separated interval collection and seeding Heng Li 2014-04-03 15:10:50 -0400
  • 9a5705289c added more debugging infomation Heng Li 2014-04-03 13:38:08 -0400
  • 3efb7c0e91 r455: release bwa-0.7.8 Heng Li 2014-03-31 15:27:23 -0400
  • 127c00cc96 dev-454: wording change in command line prompt Heng Li 2014-03-31 12:03:27 -0400
  • b27bdf1ae0 dev-453: change of -A scales -TdBOELU Heng Li 2014-03-31 11:52:52 -0400
  • b7076d9023 dev-r452: allow to specify insert size at cmd Heng Li 2014-03-31 11:21:03 -0400
  • 417c6d66c7 dev-r451: fixed a few bugs when -A!=1 Heng Li 2014-03-31 10:52:45 -0400
  • 9ce50a4e5e dev-450: support diff ins/del penalties. NO TEST!! Heng Li 2014-03-28 14:54:06 -0400
  • 578bb55c38 dev-449: unequal ins/del in global() and extend() Heng Li 2014-03-28 14:15:38 -0400
  • 0c783399e8 dev-448: different ins/del penalties Heng Li 2014-03-28 10:54:23 -0400
  • 8f9aeef4ec Merge branch 'master' into dev Heng Li 2014-03-17 00:03:52 -0400
  • e6931bec03 r445: unnecessarily large bandwidth in global Heng Li 2014-03-17 00:01:00 -0400
  • 7d63e76245 r444: more debugging output in CIGAR generation Heng Li 2014-03-16 23:25:04 -0400
  • 8929bd1c25 r443: more verbose debugging information Heng Li 2014-03-16 15:18:58 -0400
  • 8ede4ffbfa Fixed clang compiling warnings Heng Li 2014-03-16 15:18:22 -0400
  • 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