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  • 2848d3045a more accurate chain weight Heng Li 2013-02-08 15:34:25 -0500
  • 220fc39e9d the previous change does not work... Fixed. Heng Li 2013-02-08 14:51:24 -0500
  • fdb0a7405f better dealing with microrepeat Heng Li 2013-02-08 14:46:57 -0500
  • 057b292dde exclude identical hits Heng Li 2013-02-08 14:18:39 -0500
  • 1bf1a674a8 minor improvement to mapQ Heng Li 2013-02-08 13:43:15 -0500
  • 245505deed minor improvement to mapQ approx. Heng Li 2013-02-07 22:09:58 -0500
  • d8e4d57956 Don't use narrow band. Heng Li 2013-02-07 21:22:54 -0500
  • d890c7997c better treatment for micro-repeat Heng Li 2013-02-07 21:20:36 -0500
  • 45b0d3423a bugfix: when no seed hits found Heng Li 2013-02-07 20:07:31 -0500
  • cd6bd524d4 discard internal seeds shorter than half Heng Li 2013-02-07 19:50:37 -0500
  • 83a49f3210 compute mapQ; extend from the longest seed Heng Li 2013-02-07 17:15:45 -0500
  • 6ba11ab68c no effective changes Heng Li 2013-02-07 16:42:01 -0500
  • ff3fea115c write soft clip; added debugging code Heng Li 2013-02-07 16:27:11 -0500
  • 27fdf6397d single-end working! no mapQ, though Heng Li 2013-02-07 15:52:36 -0500
  • 49f2bcc015 CIGAR is wrong, but the rest is okay Heng Li 2013-02-07 14:57:22 -0500
  • 1fd51fc3f7 code backup Heng Li 2013-02-07 14:36:18 -0500
  • bfeb37c4de code backup Heng Li 2013-02-07 13:29:01 -0500
  • 5dc398cdef start to write CLI Heng Li 2013-02-07 13:13:43 -0500
  • a09db69037 In bwtsw, replace the batch seq-reader with bseq Heng Li 2013-02-06 17:12:27 -0500
  • 901d28d5f5 code backup Heng Li 2013-02-06 15:03:09 -0500
  • 5a0b32bfd2 updated to the latest kseq.h Heng Li 2013-02-06 14:38:40 -0500
  • a9292d674d a bit code cleanup Heng Li 2013-02-06 13:59:32 -0500
  • e65b2096f7 removed useless members Heng Li 2013-02-06 12:25:49 -0500
  • 797a8c147e sorting chains while filtering chains Heng Li 2013-02-05 21:58:33 -0500
  • a61288c768 separate CIGAR generation Heng Li 2013-02-05 21:49:19 -0500
  • 14e6a7bdb9 fixed a silly bug in ksw_extend() Heng Li 2013-02-05 17:29:03 -0500
  • 1e16f3e701 calling ksw_global(); ksw_extend() is buggy! Heng Li 2013-02-05 17:13:12 -0500
  • 86caae811e added comments Heng Li 2013-02-05 16:58:35 -0500
  • 1bc9712cd8 explicitly use bit to keep bt matrix Heng Li 2013-02-05 16:28:15 -0500
  • 7e1466c885 implemented NW backtrack Heng Li 2013-02-05 16:05:53 -0500
  • d91e320972 towards reimplementing banded NW alignment Heng Li 2013-02-05 12:06:56 -0500
  • 7067af833d fixed a silly bug on sorted merge Heng Li 2013-02-05 00:41:07 -0500
  • d6a73c9171 chain filtering apparently working Heng Li 2013-02-05 00:17:20 -0500
  • 9d0cdb2d3c unfinished chain filter Heng Li 2013-02-04 17:23:06 -0500
  • c589b42fb5 minor tuning for fewer identical hits Heng Li 2013-02-04 16:48:11 -0500
  • 29c8546679 better ref extraction Heng Li 2013-02-04 16:08:00 -0500
  • 788e9d1e3d fixed a couple of leaks; buggy atm Heng Li 2013-02-04 15:40:26 -0500
  • f27bd18f20 check if every seed is included; not used for now Heng Li 2013-02-04 15:09:47 -0500
  • 5bfa45a69b write the mem_aln_t struct Heng Li 2013-02-04 15:02:56 -0500
  • 666638a953 changed the default scoring Heng Li 2013-02-04 14:51:51 -0500
  • ba18db1a9f sw extension works for the simplest case Heng Li 2013-02-04 12:37:38 -0500
  • f83dea36d8 no effective changes Heng Li 2013-02-03 18:16:43 -0500
  • 2093398231 bugfix: the first line is wrong Heng Li 2013-02-03 17:47:57 -0500
  • e8a1962efe code backup; it is wrong Heng Li 2013-02-03 17:25:40 -0500
  • 92b084e553 reimplemented SW extension; not tested yet Heng Li 2013-02-02 16:38:21 -0500
  • d25a87cc50 code backup Heng Li 2013-02-02 15:14:24 -0500
  • 00e5302219 routine to get subsequence from 2-bit pac Heng Li 2013-02-01 16:39:50 -0500
  • 7ab4b3321f bugfix: memory leak Heng Li 2013-02-01 15:26:34 -0500
  • f8f3b7577a code cleanup; added a missing file Heng Li 2013-02-01 14:38:44 -0500
  • 620ad6e5b9 reseed long SMEMs Heng Li 2013-02-01 14:20:38 -0500
  • abc675f278 typo in comments Heng Li 2013-02-01 13:14:16 -0500
  • 86f2e134ba no effective changes Heng Li 2013-02-01 12:57:48 -0500
  • 5d372cef65 bugfix: wrong B-tree comparison Heng Li 2013-01-31 16:39:24 -0500
  • 8977737460 basic chaining working Heng Li 2013-01-31 16:26:05 -0500
  • 6c19c9640c code backup Heng Li 2013-01-31 15:55:22 -0500
  • 91debf412b move smem iterators to bwamem.{c,h} Heng Li 2013-01-31 13:59:48 -0500
  • 5a4a0c4173 a bit refactoring for further changes Heng Li 2013-01-31 12:34:05 -0500
  • 6de74888fd bugfix: min_intv not working in SMEM Heng Li 2013-01-31 12:12:58 -0500
  • 543c719a54 fixed a couple of unimportant bugs in SMEM Heng Li 2013-01-31 11:53:07 -0500
  • 6641788d38 preparation for further changes Heng Li 2013-01-31 11:42:31 -0500
  • 4f4e998d7f Added wrappers for fputc and fputs; more efficient sequence printing Rob Davies 2013-01-09 14:43:36 +0000
  • 55f1b36534 New wrapper for gzclose; added err_fflush calls and made it call fsync too. Rob Davies 2013-01-03 16:57:37 +0000
  • b081ac9b8b Use wrapper functions to catch system errors Rob Davies 2012-12-16 10:34:57 +0000
  • 752ce69b78 Added more wrappers for functions that make system calls Rob Davies 2012-12-16 10:05:32 +0000
  • 292f9061ab r132: optionally copy FASTA/Q comment to SAM Heng Li 2012-10-26 12:54:32 -0400
  • 3abfd0743a r131: r128 plus remote changes Heng Li 2012-06-28 14:52:18 -0400
  • fa51f029b9 Merge branch 'master' of github.com:lh3/bwa Heng Li 2012-06-28 14:51:51 -0400
  • f44edd4fc9 r128: more conservative chaining filter Heng Li 2012-06-28 14:51:02 -0400
  • 0ae318be0d resolve duphits after right extension as well Heng Li 2012-06-28 13:32:58 -0400
  • f89649ee26 Merge pull request #11 from sjackman/inline Heng Li 2012-06-26 07:02:49 -0700
  • 84d34e1d0b Do not inline functions used externally Shaun Jackman 2012-06-25 12:48:43 -0700
  • 09ee115dcc r126: release bwa-0.6.2 Heng Li 2012-06-19 13:29:44 -0400
  • 29ed2d8287 rename the "api" branch as "master" Heng Li 2012-06-19 13:13:29 -0400
  • d97ff6bf72 r124: updated version number Heng Li 2012-04-17 20:45:07 -0400
  • 72f1a95448 Merge branch 'master' into api Heng Li 2012-04-17 20:44:30 -0400
  • cd818687ac r115: added -I and -S to bwasw Heng Li 2012-04-17 20:43:43 -0400
  • 4f61e2b7f5 unnecessary large .sai output Heng Li 2012-04-17 19:31:37 -0400
  • 9c486fa41e updated APIs abit Heng Li 2012-04-08 00:55:52 -0400
  • 3b5a9e5595 simplified bwa_se() interface Heng Li 2012-04-08 00:12:34 -0400
  • ca93a71e6e complete single-end alignment Heng Li 2012-04-08 00:02:06 -0400
  • 080726cb47 preliminary doc Heng Li 2012-04-07 22:50:07 -0400
  • 1cef219667 compute CIGAR; rev seq not working Heng Li 2012-04-07 22:00:03 -0400
  • 66154ff5d2 towards refined gapped; unfinished Heng Li 2012-04-07 01:25:39 -0400
  • a1abfe9977 API: aln seems working Heng Li 2012-04-07 00:23:01 -0400
  • cff473393c commented out debugging code Heng Li 2012-04-02 12:05:15 -0400
  • 790df95e1a updated revision number Heng Li 2012-04-02 11:43:32 -0400
  • 36f2fd6238 bugfix: incorrect bandwidth Heng Li 2012-04-02 11:39:40 -0400
  • d3169804f6 debugging; bug persistant Heng Li 2012-04-02 10:45:42 -0400
  • 173b93dfd4 debugging code: bwasw has a rare bug Heng Li 2012-04-02 09:37:02 -0400
  • d33abf127f check *.64.bwt first and then *.bwt Heng Li 2012-03-29 14:45:00 -0400
  • c875085b2b do not use .64 suffix by default Heng Li 2012-03-29 12:31:01 -0400
  • bdc953cad9 Tim's suggestion suffix file name with .64 Heng Li 2012-03-29 12:22:51 -0400
  • a471f1918b bugfix: long-existing out-of-boundary bug Heng Li 2012-03-19 13:45:09 -0400
  • 91a4a0c8ea Release bwa-0.6.1 Heng Li 2011-11-28 09:52:07 -0500
  • 64e353ce49 bugfix: bwa-sw PE segfault in rare case Heng Li 2011-11-28 09:12:21 -0500
  • bf65b6463a fastmap: optionally output the original query seq Heng Li 2011-11-24 19:44:21 -0500
  • 150bfbdef4 fixed a deadlock; SMEM iterator Heng Li 2011-11-24 19:15:14 -0500
  • b5170e0efa output the NM tag Heng Li 2011-11-24 11:51:38 -0500
  • 717959e819 fixed a minor issue in trimming Heng Li 2011-11-24 10:39:41 -0500
  • eeedda105d perhaps improves samse/sampe Heng Li 2011-11-24 01:22:02 -0500