zzh
/
bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Commit Graph

  • 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
  • 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