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  • d9f654908f Merge pull request #30 from mp15/header_hd Heng Li 2014-08-26 09:44:29 -0400
  • ec55ed8d83 Add @HD tag to SAM header Martin O. Pollard 2014-08-26 12:04:54 +0100
  • b5cba257c1 r809: new strategy for the -a mode Heng Li 2014-08-25 11:59:27 -0400
  • bf7d1d46ca r808: a minor bug with the new index -b Heng Li 2014-08-25 10:36:24 -0400
  • 1bba5ef20e r807: allow to change block size in bwt_gen Heng Li 2014-08-25 10:31:54 -0400
  • 1de61b556e r806: polish BAM support Heng Li 2014-08-08 13:36:56 -0400
  • 8a230db596 Merge branch 'nh_bam_support' of git://github.com/nh13/bwa into nh13-nh_bam_support Heng Li 2014-08-08 13:12:54 -0400
  • b73f4c977a Merge branch 'master' into new-master Heng Li 2014-08-07 21:51:58 -0400
  • 0a6f2660b4 Fixed a bug related to the score returned. Mustafa Ozdal 2014-08-07 13:50:42 -0700
  • c1df343740 Merge branch 'master' of github.com:lh3/bwa Mustafa Ozdal 2014-08-07 13:49:01 -0700
  • 9bdcf31dec don't process hard clipped SEQ Heng Li 2014-08-07 10:36:28 -0400
  • a1a57d97be r796: more debugging code Heng Li 2014-08-07 14:58:51 -0400
  • d9dfab2ba2 r795: intel's ksw_extend() replacement Heng Li 2014-08-07 13:43:07 -0400
  • b5415ba23d first integration; compiled, but NOT TESTED! Heng Li 2014-08-07 11:59:37 -0400
  • 5e56bec0f4 don't process hard clipped SEQ Heng Li 2014-08-07 10:36:28 -0400
  • 482a47a57e adding support for SAM/BAM output using htslib. Please turn on within the Makefile. Nils Homer 2014-06-04 10:29:32 -0400
  • 705aa53894 Released 0.7.10 Heng Li 2014-07-13 22:57:27 -0400
  • 7fd6a11569 r788: segfault when the last ref is "weird" Heng Li 2014-07-10 10:53:56 -0400
  • cffff4338f r787: use mem_seed_sw() also for non-PacBio reads Heng Li 2014-07-10 10:30:22 -0400
  • 3efc33160c 0.7.9a-r786: fixed a segfault in a rare case Heng Li 2014-05-19 16:47:25 -0400
  • 031d3d83ce Wrong release number: 0.7.8 => 0.7.9 Heng Li 2014-05-19 09:49:26 -0400
  • be74dbc00c Release bwa-0.7.9-r783 Heng Li 2014-05-19 09:09:11 -0400
  • e4752b321b Release bwa-0.7.9-r782 Heng Li 2014-05-19 09:08:07 -0400
  • f00cc94e1d r779: fixed a memory leak in SE Heng Li 2014-05-16 00:06:34 -0400
  • a5ad0cff7f r778: reduced the number of alloc() calls a bit Heng Li 2014-05-15 23:23:04 -0400
  • 012d54fc49 Updated release notes Heng Li 2014-05-15 11:48:28 -0400
  • 8d2986ece2 r770: fixed a compiling warning Heng Li 2014-05-14 14:44:03 -0400
  • 8f3e7d573b fixed wrong FAQ links Heng Li 2014-05-14 14:36:52 -0400
  • d67e923026 changed the heading format Heng Li 2014-05-14 14:33:42 -0400
  • 1627f9dfae updated README Heng Li 2014-05-14 14:32:09 -0400
  • 061c63f36a r766: removed useless code Heng Li 2014-05-13 13:09:29 -0400
  • 0168f39eeb r765: fixed a declaration error Heng Li 2014-05-13 12:54:23 -0400
  • 08517ac09b r764: changed -c in "-x pacbio" to 500 Heng Li 2014-05-13 12:53:24 -0400
  • a35a6c2580 updated maual page Heng Li 2014-05-12 12:52:16 -0400
  • 39a6cd5bb0 r762: cleanup for the new release; unfinished Heng Li 2014-05-11 15:15:44 -0400
  • cfe6996173 r760: removed commented code Heng Li 2014-05-09 14:59:07 -0400
  • 43b498a37e r759: bugfix - frac_rep not working Heng Li 2014-05-09 14:56:59 -0400
  • c9b33502f3 r758: fixed a typo Heng Li 2014-05-07 15:07:29 -0400
  • e56572e88f help on how to use bwa-helper.js Heng Li 2014-05-06 17:11:17 -0400
  • 1ced2f386c more debugging info at -v5 Heng Li 2014-05-06 16:35:40 -0400
  • 4b951592fb download link of data used by genalt Heng Li 2014-05-06 16:29:20 -0400
  • 6ac8dd5840 r754: added command msg for -h Heng Li 2014-05-06 16:15:14 -0400
  • 81970e7687 more comments Heng Li 2014-05-06 16:12:22 -0400
  • c50ee8c841 genalt is working Heng Li 2014-05-06 16:02:40 -0400
  • 8d37726325 code backup Heng Li 2014-05-06 11:57:02 -0400
  • 024195db62 code backup Heng Li 2014-05-05 16:51:14 -0400
  • ce3c198245 r749: max_hits tunable on CMD; default to 5 Heng Li 2014-05-04 10:17:03 -0400
  • f21d6498bc r748: reduced the default -m to 50 Heng Li 2014-05-02 16:49:19 -0400
  • e8f28cb529 r747: fixed a minor issue in the last (mis)commit Heng Li 2014-05-02 16:17:50 -0400
  • 6db761e269 r746: tuned heuristic for GRCh38 Heng Li 2014-05-02 16:06:27 -0400
  • 8763e0ced7 Helpful scripts Heng Li 2014-05-02 10:43:49 -0400
  • b7076848ab r744: int overflow given MB query Heng Li 2014-05-01 15:30:36 -0400
  • fa20c71920 r742: further control the max bandwidth Heng Li 2014-05-01 14:27:38 -0400
  • 7954e77a1b r741: fixed segfault in rare cases Heng Li 2014-05-01 11:13:05 -0400
  • 4b2441069f r740: don't attempt merge if bandwidth too large Heng Li 2014-05-01 11:01:52 -0400
  • 5aedc978d1 r739: output suboptimal hits in the PE mode Heng Li 2014-04-30 23:23:54 -0400
  • c6c943f9d7 r738: output multi-map in the XA tag (SE only) Heng Li 2014-04-30 16:46:05 -0400
  • d59d78838c r737: fixed an assertion when failed to convert sa Heng Li 2014-04-30 14:55:44 -0400
  • 88f89be60e r736: improved in low-complexity regions Heng Li 2014-04-30 14:14:20 -0400
  • 11698fc4e5 r735: fixed a bug caused by merge Heng Li 2014-04-30 13:12:43 -0400
  • b603fed39c r733: bugfix - seed score unset when no -W Heng Li 2014-04-29 14:58:53 -0400
  • 44754cd615 r731: separate layouter Heng Li 2014-04-28 10:39:29 -0400
  • dadd5d6281 r730: more permissive about merging overlapping Heng Li 2014-04-28 10:01:54 -0400
  • 76bb49e01b r729: halved band width; doubled patch band width Heng Li 2014-04-24 16:06:01 -0400
  • 6052d3015b r728: sorting the end in mem_sort_dedup_patch() Heng Li 2014-04-24 15:44:59 -0400
  • df65893fb5 r727: extend seeds with SW Heng Li 2014-04-24 14:28:40 -0400
  • b92bbb47e5 Merge branch '0.7.7-softclip' into layout Heng Li 2014-04-24 12:24:49 -0400
  • 8c12ec4a4b r725: optionally disable hard clipping Heng Li 2014-04-24 11:56:43 -0400
  • 954cfd766d improved ksw_extend2() Heng Li 2014-04-23 15:14:52 -0400
  • b93fca2b2e r723: merge adjacent hits Heng Li 2014-04-16 16:38:50 -0400
  • 48847af2fc code backup Heng Li 2014-04-16 12:00:13 -0400
  • 00a07f61bf r721: merge overlapping hits by default Heng Li 2014-04-15 16:16:04 -0400
  • 45f24b4ae8 r720: improved overlap hit merging Heng Li 2014-04-15 16:09:42 -0400
  • bdb7b000cd r719: more stringent overlap merge Heng Li 2014-04-15 14:52:17 -0400
  • 4e22270eba r718: merge alnregs overlapping on both query/ref Heng Li 2014-04-14 17:01:17 -0400
  • a38b065642 Merge branch 'master' into layout Heng Li 2014-04-14 16:05:08 -0400
  • 6d4a6debdc r716: changed -x pbread Heng Li 2014-04-14 16:04:29 -0400
  • 1209f161c9 code backup Heng Li 2014-04-14 12:24:45 -0400
  • 836d464239 r713: a bug in retrieving ref seq on rev Heng Li 2014-04-14 09:55:55 -0400
  • d5877ad0a9 code backup Heng Li 2014-04-14 09:33:45 -0400
  • f2b7d67ed9 output extra debugging information Heng Li 2014-04-13 12:51:44 -0400
  • c9645579bd code backup Heng Li 2014-04-13 12:49:10 -0400
  • 685cd235a6 better readability for the neighbor struct Heng Li 2014-04-11 11:24:08 -0400
  • 42e2a7ad46 fixed a bug in overlap type inferrence Heng Li 2014-04-11 11:14:06 -0400
  • bbcabfe342 r707: change params for pacbio-to-pacbio Heng Li 2014-04-10 21:53:52 -0400
  • 658f27eae4 Merge branch 'dev' into layout Heng Li 2014-04-10 21:48:47 -0400
  • 6fda93502f r705: pairing performed on one chr only Heng Li 2014-04-10 21:38:14 -0400
  • db4b171fa6 Merge branch 'dev' into layout Heng Li 2014-04-10 21:09:47 -0400
  • 07182d9061 dev-475: -F outputs unit score, not raw score Heng Li 2014-04-10 21:09:06 -0400
  • 7d25fe2de3 Merge branch 'dev' into layout Heng Li 2014-04-10 21:07:16 -0400
  • e80bccc923 dev-474: fixed a typo Heng Li 2014-04-10 21:04:02 -0400
  • f02cd42679 dev-473: added a few assertions Heng Li 2014-04-10 21:03:13 -0400
  • 8638cfadc8 dev-472: get rid of bwa_fix_xref() Heng Li 2014-04-10 20:54:27 -0400
  • e2d0c996e9 layout-477: output unit score, not the raw score Heng Li 2014-04-10 18:03:28 -0400
  • 0eeacbbe39 Merge branch 'dev' into layout Heng Li 2014-04-10 17:56:24 -0400
  • 23e0e99ec0 dev-471: fixed a compiling error from last commit Heng Li 2014-04-10 11:54:17 -0400
  • ccbbe48c4f dev-470: don't stop on bwa_fix_xref2() failures Heng Li 2014-04-10 11:43:17 -0400
  • 22c1d3cecc code backup Heng Li 2014-04-10 10:34:57 -0400
  • cf6661a8fe code backup Heng Li 2014-04-09 23:41:39 -0400
  • bcf6d1b355 code backup Heng Li 2014-04-09 16:49:37 -0400