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  • 15becdd3df use weight1 by default Heng Li 2014-10-14 14:50:37 -0400
  • df20911110 r890: bns_intv2rid() may wrongly return -1 Heng Li 2014-10-14 14:49:53 -0400
  • 2485a3ca02 bug in the last commit Heng Li 2014-10-12 18:24:40 -0400
  • bf08f76a3c requiring full overlap Heng Li 2014-10-12 17:17:29 -0400
  • 4356fd485c changed weighting Heng Li 2014-10-10 13:41:53 -0400
  • 2d7ec6b051 ALT genotyping semi-working, but ... Heng Li 2014-10-05 22:18:07 -0400
  • 2c3619d569 code backup Heng Li 2014-10-02 23:48:03 -0400
  • 7026b3ec68 code backup Heng Li 2014-10-02 21:49:29 -0400
  • cd44ac48cd code backup Heng Li 2014-10-02 18:04:36 -0400
  • c4bdf1678d code backup Heng Li 2014-10-02 17:11:37 -0400
  • 0a526c698a code backup Heng Li 2014-10-02 16:23:55 -0400
  • 7b62fbb4ba r880: bug in writing .ann file Heng Li 2014-10-02 15:34:49 -0400
  • d802cfb7f5 code backup Heng Li 2014-09-30 20:50:26 -0400
  • a03d01f944 r878: XA is given to the best alignment Heng Li 2014-09-30 13:50:51 -0400
  • 039ea20639 Merge branch 'dev' Heng Li 2014-09-27 23:22:18 -0400
  • 0a2cf98293 r876: optionally ignore idxbase.alt file Heng Li 2014-09-27 23:21:50 -0400
  • dae4ca3ced r875: invalid SAM output for ALT hits Heng Li 2014-09-26 15:29:08 -0400
  • 8d61316cc8 more comments Heng Li 2014-09-23 10:33:15 -0400
  • e8e5bbc071 Merge branch 'dev' Heng Li 2014-09-19 23:56:19 -0400
  • 5fc0f44e27 mapQ is not quite right Heng Li 2014-09-19 23:39:59 -0400
  • a33ca20499 separate postalt to a separate script Heng Li 2014-09-19 23:23:54 -0400
  • fd42d30910 Merge branch 'dev' Heng Li 2014-09-19 17:05:59 -0400
  • 23bc50e240 removed altlift; suppress primary hit by default Heng Li 2014-09-19 17:05:27 -0400
  • 7426a750ec r868: use soft clip for ALT hits Heng Li 2014-09-19 16:58:18 -0400
  • 9af36064e8 r867: fixed a few bugs; added ALT hits to XA Heng Li 2014-09-19 16:50:21 -0400
  • 7cbcbc4abf Merge branch 'dev' Heng Li 2014-09-18 11:54:41 -0400
  • b22bed2b5e removed <> from markdown Heng Li 2014-09-18 11:54:23 -0400
  • 954ee5eda9 Merge branch 'dev' Heng Li 2014-09-18 11:52:03 -0400
  • 030825ae85 updated release notes Heng Li 2014-09-18 11:51:52 -0400
  • ba7ed47d40 error in altpost Heng Li 2014-09-18 11:18:10 -0400
  • 70e9ed0ea9 Merge branch 'dev' Heng Li 2014-09-18 10:50:07 -0400
  • a41afe4c97 These files were committed on a wrong branch Heng Li 2014-09-18 10:49:35 -0400
  • dd1c6619d7 r858: bugfix in PE alt alignments Heng Li 2014-09-18 10:47:21 -0400
  • b9026ecafd Merge branch 'dev' Heng Li 2014-09-17 23:18:09 -0400
  • a32d44d8d6 r855: show ALT hits in the PE mode, too Heng Li 2014-09-17 23:07:56 -0400
  • c982443210 r854: improved the calculation of pa Heng Li 2014-09-17 16:26:28 -0400
  • d677a4325b Merge branch 'dev' Heng Li 2014-09-17 14:22:20 -0400
  • f5a0e576e6 added postalt to bwa-helper for post processing Heng Li 2014-09-17 14:18:40 -0400
  • 825ae92e58 r849: the pa tag now gives a number Heng Li 2014-09-17 13:05:35 -0400
  • 6f37c14f26 r848: tag alignments with primary ALT Heng Li 2014-09-16 18:52:49 -0400
  • 945d39fb79 Merge branch 'dev' Heng Li 2014-09-16 14:39:33 -0400
  • a458442b24 r845: updated NEWS Heng Li 2014-09-16 14:38:41 -0400
  • 92bc6849a3 r844: added intra-species contig mapping mode Heng Li 2014-09-16 10:53:07 -0400
  • 90518f11e3 r843: presetting for ONT 2d reads Heng Li 2014-09-16 10:38:15 -0400
  • 152d25ff87 Merge branch 'dev' Heng Li 2014-09-16 10:17:53 -0400
  • 230cd16712 updated dependency Heng Li 2014-09-16 10:17:30 -0400
  • d0af3648d1 Fixed a typo Heng Li 2014-09-16 10:16:45 -0400
  • 1bdd791539 r837: removed BAM support Heng Li 2014-09-16 09:57:35 -0400
  • 7244d66833 r836: a dangerous merge Heng Li 2014-09-16 00:37:58 -0400
  • df09f38ad3 Merge branch 'dev' Heng Li 2014-09-16 00:24:41 -0400
  • 43ce69104d Removed PacBio read-to-read instruction Heng Li 2014-09-15 23:59:35 -0400
  • d013ea94b0 Removed instruction on ALT alignment Heng Li 2014-09-15 23:45:17 -0400
  • 4b6eeb34c8 r830: optionally fixed chunk size Heng Li 2014-09-15 23:42:24 -0400
  • 624687b072 r829: killed a harmless gcc warning Heng Li 2014-09-15 23:33:22 -0400
  • 5d26ab0ee3 r828: changed the default scoring for pacbio Heng Li 2014-09-15 23:22:05 -0400
  • 41b137d202 Merge pull request #32 from mmoisse/patch-1 Heng Li 2014-09-15 22:59:22 -0400
  • b07587f806 r827: an alt hit as good as a pri hit as supp Heng Li 2014-09-15 16:07:51 -0400
  • bd85af08ab r826: improved alt mapping for PE Heng Li 2014-09-15 12:13:04 -0400
  • aee53f1334 r824: ALT mapping seems working Heng Li 2014-09-15 00:29:05 -0400
  • 015ab3f6c3 r823: towards ALT support Heng Li 2014-09-14 16:41:14 -0400
  • 8116bcc786 Merge branch 'dev' into alt Heng Li 2014-09-14 15:40:52 -0400
  • dfd8c9eeb6 Update README.md mmoisse 2014-09-14 11:26:39 +0200
  • 8d2b93156b r821: more relax on containing seeds Heng Li 2014-09-12 10:35:49 -0400
  • 6739b713dd Merge branch 'hotfix-utgaln' into dev Heng Li 2014-09-08 12:44:42 -0400
  • f4aedddee6 r819: bugfix - added too many sub-SMEMs Heng Li 2014-09-08 11:32:48 -0400
  • ca61fe3ad5 code backup Heng Li 2014-09-08 08:52:02 -0400
  • 1934f0cf24 code backup Heng Li 2014-09-05 13:20:52 -0400
  • e4ad616d43 r816: read .alt file (not tested) Heng Li 2014-09-05 12:49:50 -0400
  • 35ac99b4f7 r815: optionally output ref fasta header Heng Li 2014-08-29 10:51:23 -0400
  • c7679ee781 Merge pull request #31 from jwbargsten/master Heng Li 2014-08-29 10:22:11 -0400
  • 9c5fd803e9 wrong function to print @HD line in bwa_print_sam_hdr Joachim Bargsten 2014-08-29 11:51:07 +0200
  • 1e611b235c r810: add err_puts() Heng Li 2014-08-26 11:07:24 -0400
  • 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