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  • 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
  • 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