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  • 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
  • 196b50dde3 optionally mark multi-part hits as secondary Heng Li 2011-11-23 23:39:59 -0500
  • 9f84384ed2 reordering BWA-SW command-line prompt Heng Li 2011-11-23 23:36:08 -0500
  • b17b6577ac removed a useless bwa-sw CMD option Heng Li 2011-11-23 23:30:14 -0500
  • 107a9870ef incorrect mate pos in BWA-SW SE mode Heng Li 2011-11-23 23:18:51 -0500
  • dec584d50b fixed a long-existing bug in trimming Heng Li 2011-11-23 23:11:50 -0500
  • 84aa3fa696 useless script Heng Li 2011-11-19 21:48:54 -0500
  • 182cb2e89c use standard SW when no SSE2 Heng Li 2011-11-19 19:38:21 -0500
  • dc4008936c avoid duplicated XA tags Heng Li 2011-11-19 14:52:47 -0500
  • 8f89f55484 fixed a segfault when there are too few good bases. Heng Li 2011-11-17 22:13:38 -0500
  • c8edcafb44 added SEAL Heng Li 2011-11-12 20:48:35 -0500
  • 162f220deb updated README Heng Li 2011-11-12 20:26:52 -0500
  • 9f2c77880d remove a useless file Heng Li 2011-11-12 20:06:37 -0500
  • 770a5f2ae0 Release BWA-0.6.0 Heng Li 2011-11-12 20:04:39 -0500
  • f1517b845c updated manual Heng Li 2011-11-12 18:35:04 -0500
  • 7544aca718 updated revision number Heng Li 2011-11-12 16:56:21 -0500
  • 2f3cdcd55b bugfix: bwa-short MT does not work (by Peter) Heng Li 2011-11-12 16:54:38 -0500
  • 56a18659b6 crash under non-typical setting (by John Marshall) Heng Li 2011-11-12 16:53:53 -0500
  • 8060693411 multithreading works again Heng Li 2011-11-12 16:50:58 -0500
  • fa8cfe5567 bugfix: wrong mapping quality Heng Li 2011-11-12 12:12:45 -0500
  • b42910ada6 proper mate information Heng Li 2011-11-12 00:49:21 -0500
  • e06685db45 bwa-sw PE seems working (SAM is incorrect) Heng Li 2011-11-07 00:51:43 -0500
  • c8c79ef024 mate rescue seems working (not MT) Heng Li 2011-11-06 16:20:40 -0500
  • 17eaac5a21 compute insert size distribution Heng Li 2011-11-05 23:17:52 -0400
  • a29b179045 further preparation for pairing Heng Li 2011-11-05 14:31:30 -0400
  • 06687a33b9 bwasw: read and align two fastq at a time Heng Li 2011-11-05 14:00:01 -0400
  • a26096dd75 pair two single-end SAMs Heng Li 2011-11-05 10:56:25 -0400
  • 4083fe9413 fixed a typo Heng Li 2011-11-02 09:03:05 -0400
  • 673ae4aaf8 throw an error if insufficient memory during index Heng Li 2011-10-31 13:26:24 -0400