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  • c4ac1bee88 added Travis CI integration Heng Li 2014-10-17 17:02:26 -0400
  • fa50c1b77f Merge branch 'dev' Heng Li 2014-10-17 16:39:24 -0400
  • 1b2eb4c9ab added travis CI Heng Li 2014-10-17 16:39:14 -0400
  • d0a796b644 moved bwashm.o to AOBJS Heng Li 2014-10-17 16:23:35 -0400
  • c8ae5029b3 minor change to example Heng Li 2014-10-17 16:19:21 -0400
  • a06646493b r915: fixed broken example.c Heng Li 2014-10-17 16:17:28 -0400
  • a55aac8a43 added section about the completeness of GRCh38 Heng Li 2014-10-17 15:42:17 -0400
  • 6deafdadca Merge branch 'dev' Heng Li 2014-10-17 12:14:40 -0400
  • 8af17b3478 r912: very minor improvement Heng Li 2014-10-17 12:14:18 -0400
  • c280274331 r911: check before attempting adding Heng Li 2014-10-17 12:13:09 -0400
  • 44a185f2c1 Merge branch 'dev' Heng Li 2014-10-17 09:43:52 -0400
  • 67c2d69218 made the header smaller Heng Li 2014-10-16 17:17:02 -0400
  • fab1f2b561 README on ALT mapping Heng Li 2014-10-16 17:15:39 -0400
  • 76a365a95f r907: revert to -g.8 by default Heng Li 2014-10-16 15:56:33 -0400
  • d8d8b230d1 r906: don't reduce non-ALT mapQ by default Heng Li 2014-10-16 15:15:23 -0400
  • e318d8e7e5 r905: lower peak RAM for "shm -f" Heng Li 2014-10-16 11:22:09 -0400
  • ad0da1418f r904: optionally create tmp files for shm staging Heng Li 2014-10-16 10:52:59 -0400
  • 97a3102c89 r903: updated revision number Heng Li 2014-10-16 10:26:25 -0400
  • 57436ab405 added -lrt on Linux Heng Li 2014-10-15 23:23:01 -0400
  • 6804f17d38 replaced Sys V shm with POSIX shm Heng Li 2014-10-15 23:06:03 -0400
  • bfd5e1840f shm works on small files, but not large ones Heng Li 2014-10-15 15:44:06 -0400
  • 6a0952948d shared memory Heng Li 2014-10-15 14:44:08 -0400
  • c5e859b49f r898: read the index into a single memory block Heng Li 2014-10-15 12:27:45 -0400
  • c44357926f updated README, a bit Heng Li 2014-10-14 23:46:59 -0400
  • 71277f0fea r896: more flexible ALT reading Heng Li 2014-10-14 23:37:24 -0400
  • 2a18fa114f r895: increase the default max_XA_hits_alt to 200 Heng Li 2014-10-14 16:58:42 -0400
  • 647b0e828a wrong flag in the SAM output Heng Li 2014-10-14 16:57:57 -0400
  • c79427a22d improved CLI Heng Li 2014-10-14 16:31:40 -0400
  • 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