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  • efa0dd561a wrong sentence in README-alt Heng Li 2014-12-10 23:20:46 -0500
  • 9649f3496f Merge branch 'dev' Heng Li 2014-12-02 10:35:02 -0500
  • 393735d7f1 more FAQs on ALT mapping Heng Li 2014-12-02 10:30:35 -0500
  • ae4aa77b50 Merge branch 'dev' Heng Li 2014-12-01 09:51:05 -0500
  • d6e8e5929b Updated READMEs a little Heng Li 2014-12-01 09:50:47 -0500
  • 309d1c543d Merge branch 'dev' Heng Li 2014-11-26 13:27:21 -0500
  • 9d8c906e4c r1017: process I/O in a separate thread Heng Li 2014-11-26 12:32:48 -0500
  • cb8992459f Merge branch 'dev' Heng Li 2014-11-19 12:54:30 -0500
  • 3633436a3d added download link explicitly Heng Li 2014-11-19 12:54:15 -0500
  • decc812f77 Merge branch 'dev' Heng Li 2014-11-19 12:47:20 -0500
  • 6609bafa17 moved directory structure to this README Heng Li 2014-11-19 12:45:21 -0500
  • d58beeee56 smarter about path finding Heng Li 2014-11-19 12:38:55 -0500
  • 8422950472 Merge branch 'dev' Heng Li 2014-11-19 12:33:18 -0500
  • d36083bdc5 minor changes Heng Li 2014-11-19 12:33:06 -0500
  • 84024101fa minor fix to a link Heng Li 2014-11-19 12:31:32 -0500
  • 7e29a01b77 Merge branch 'dev' Heng Li 2014-11-19 12:30:03 -0500
  • 1993cb634d Split README-alt.md into two documentations Heng Li 2014-11-19 12:29:35 -0500
  • 9ade171f7a transfer read groups from the input BAM Heng Li 2014-11-19 11:43:59 -0500
  • b5f6ed3020 r1005: insert arbitrary header lines Heng Li 2014-11-19 10:59:05 -0500
  • 15c93e7a52 renamed extras to bwakit for clarity Heng Li 2014-11-19 10:37:03 -0500
  • b31992991a Merge branch 'dev' Heng Li 2014-11-19 09:37:10 -0500
  • bb7a97f68c update about bwa.kit Heng Li 2014-11-19 09:36:56 -0500
  • 82ef0500e6 Merge branch 'dev' Heng Li 2014-11-18 23:29:11 -0500
  • 56f1056b49 don't type empty files Heng Li 2014-11-18 23:28:46 -0500
  • 61ab329639 fine tune the wrapper scripts Heng Li 2014-11-18 15:40:58 -0500
  • 80e4ecfa79 r998: smart pairing; allow mixture of SE/PE reads Heng Li 2014-11-18 14:30:22 -0500
  • 6f9bf9a4ae minor change Heng Li 2014-11-17 15:23:38 -0500
  • eb664c2fe8 added an evaluation section Heng Li 2014-11-17 14:54:24 -0500
  • cee8149b12 Updated README for ALT mapping Heng Li 2014-11-17 13:20:23 -0500
  • ad9d12c04d Removed a comment on hs38 lacking EBV Heng Li 2014-11-17 11:08:07 -0500
  • bf053c779b polish Heng Li 2014-11-17 10:54:16 -0500
  • 0071c4ab22 polish the run script Heng Li 2014-11-17 10:44:54 -0500
  • 792be78a80 replace run-gen-hs38* with run-gen-ref Heng Li 2014-11-16 00:46:02 -0500
  • 050482ef77 fine tune Heng Li 2014-11-13 19:52:47 -0500
  • 65c637b036 smarter prefix finder Heng Li 2014-11-13 16:16:21 -0500
  • 4373a077d5 wrapper for bwa-mem Heng Li 2014-11-13 15:51:00 -0500
  • a5c144db4d added scripts to generate hs38a.fa and hs38d6.fa Heng Li 2014-11-13 12:53:29 -0500
  • fffe52a45b move bwa-typeHLA back to this repo Heng Li 2014-11-13 12:50:56 -0500
  • 904afefbc6 r985: fix bug due to the lack of _pri contigs d6 Heng Li 2014-11-13 12:12:41 -0500
  • c5fe18438a r984: updated to the latest kseq.h Heng Li 2014-11-13 11:12:23 -0500
  • 7eabcf42c4 r983: bugfix - wrong mate info Heng Li 2014-11-10 13:15:11 -0500
  • a81603217e mate chr is sometimes wrong Heng Li 2014-11-10 10:16:53 -0500
  • b2b42cea7e removed contig weight & code cleanup Heng Li 2014-11-07 12:45:01 -0500
  • 4e97cdfde8 move to a new project bwa-typeHLA Heng Li 2014-11-06 09:13:15 -0500
  • c2f2cb03ce to be moved to a separate project Heng Li 2014-11-06 09:12:53 -0500
  • 1bee29ef44 map to individual HLA ALT for meaningful mapQ Heng Li 2014-11-06 00:37:59 -0500
  • 10de1e0b74 optionally output debegging info Heng Li 2014-11-05 13:20:33 -0500
  • 0eee4fa1b0 nothing, really Heng Li 2014-11-04 16:00:25 -0500
  • 2a41772d0a more command line help Heng Li 2014-11-04 15:41:18 -0500
  • e5d7f4fc30 change the default max_len Heng Li 2014-11-04 15:31:33 -0500
  • ccf03ffd22 control min-match-length Heng Li 2014-11-04 15:26:10 -0500
  • de268247db type primary exons first and then the rest Heng Li 2014-11-04 15:09:21 -0500
  • 12fff1ad57 a bit code cleanup Heng Li 2014-11-04 14:30:31 -0500
  • 96fba0f2f4 proper homozygous typing; fixed a low-level bug Heng Li 2014-11-04 11:38:05 -0500
  • ace18171b0 backup Heng Li 2014-11-04 10:07:14 -0500
  • 4cbb0cb829 polished the run script Heng Li 2014-11-03 15:29:02 -0500
  • 9dbf152e31 added the pipeline script Heng Li 2014-11-03 15:16:14 -0500
  • 40c4a6ffe1 better CLI; more comments Heng Li 2014-11-03 12:09:29 -0500
  • 4bc01e90c8 not used any more Heng Li 2014-11-03 11:51:25 -0500
  • b7d0a2d537 first HLA typing script Heng Li 2014-11-03 11:47:23 -0500
  • 9bf898fa10 r963: expose mask_level Heng Li 2014-10-30 11:33:43 -0400
  • 6b4e6bf7dd Merge branch 'dev' Heng Li 2014-10-28 13:47:02 -0400
  • 6db2fd98aa r960: merge changes from the master branch Heng Li 2014-10-28 13:46:40 -0400
  • 9867634f72 r960: XA tags occasionally missing for PE Heng Li 2014-10-28 13:43:26 -0400
  • 6f39715e6e keep mate positions Heng Li 2014-10-28 13:03:33 -0400
  • 5c87869d91 keep RG Heng Li 2014-10-27 10:45:07 -0400
  • dbe74ca9b8 Merge branch 'dev' Heng Li 2014-10-25 23:10:25 -0400
  • 0f8a164bd3 bugfix: .ctw not generated properly Heng Li 2014-10-25 23:08:29 -0400
  • 2bfcc421d9 bugfix: alignments not outputted Heng Li 2014-10-25 22:13:31 -0400
  • 7327f8fa10 output all overlapping HLA hits Heng Li 2014-10-25 12:00:15 -0400
  • 33938e1ed0 save reads mapped to each HLA gene Heng Li 2014-10-24 16:54:48 -0400
  • ba3ab0ca98 removed hla typing - not good enough Heng Li 2014-10-24 14:52:16 -0400
  • 7a8019e6ee removed debugging code Heng Li 2014-10-24 14:51:05 -0400
  • 7c362bef69 added another paper Heng Li 2014-10-23 15:15:20 -0400
  • 3a1da27c1c added Bai et al. Seems good, too. Heng Li 2014-10-23 15:08:18 -0400
  • d61a1226a8 highlight Liu et al. It seems good. Heng Li 2014-10-23 14:52:48 -0400
  • b45442fbc1 Merge branch 'dev' Heng Li 2014-10-23 14:43:06 -0400
  • f005ea4bf3 coarse HLA typing and doc Heng Li 2014-10-23 14:42:45 -0400
  • af606fc31a Merge branch 'dev' Heng Li 2014-10-22 16:17:36 -0400
  • 3d129be642 r943: change the default -y to 20, but ... Heng Li 2014-10-22 12:42:58 -0400
  • 4177d6c2c7 r942: ignore ALT hits when counting n_sub for ... Heng Li 2014-10-22 10:24:16 -0400
  • 60b728487a r941: set a min length for 3rd-round seeding Heng Li 2014-10-21 13:15:42 -0400
  • 282130a64e r940: fixed a bug - missing primary hit Heng Li 2014-10-21 12:57:49 -0400
  • 5e00d08346 r939: fixed a memory leak (issue #35) Heng Li 2014-10-21 09:26:19 -0400
  • 574098d034 updated directory name Heng Li 2014-10-21 00:57:06 -0400
  • acf4922fe4 Merge branch 'dev' Heng Li 2014-10-21 00:55:19 -0400
  • 4260699a09 updated ALT readme due to recent changes Heng Li 2014-10-21 00:55:00 -0400
  • e3adc4275b Merge branch 'dev' Heng Li 2014-10-21 00:23:39 -0400
  • 76a15ea91b r933: with bwa-postalt ready, drop option -g Heng Li 2014-10-21 00:23:14 -0400
  • 2bfa3c767b CLI help Heng Li 2014-10-21 00:22:59 -0400
  • 497913d404 working largely as expected Heng Li 2014-10-21 00:16:41 -0400
  • a6b5a30dab r930: use 3rd round seeding by default Heng Li 2014-10-20 17:34:15 -0400
  • 038af2a551 r929: added simplified LAST-like seeding Heng Li 2014-10-20 17:00:31 -0400
  • 25d45512d9 code backup Heng Li 2014-10-20 14:17:56 -0400
  • 6f41a27e27 towards adding "-r" to postprocessing Heng Li 2014-10-19 20:53:47 -0400
  • 3370ae9e35 r926: prepare to move -g to bwa-postalt.js Heng Li 2014-10-19 20:43:53 -0400
  • 6e13694721 removed coverity Heng Li 2014-10-17 21:46:11 -0400
  • e65dc133f4 updated Travis CI link Heng Li 2014-10-17 21:34:43 -0400
  • f968b4b73d added drone build Heng Li 2014-10-17 21:28:44 -0400
  • 059c8eb899 for coverity Heng Li 2014-10-17 21:03:11 -0400