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  • 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
  • 02946df28a fixed a off-by-1 bug Heng Li 2011-10-27 13:55:48 -0400
  • 7babb54e4c drop smem based mapping algorithm Heng Li 2011-10-27 10:56:09 -0400
  • 7467671c30 minor change Heng Li 2011-10-25 21:39:38 -0400
  • e890b8ac2e preliminary code to generate fake sam Heng Li 2011-10-25 19:45:55 -0400
  • 55059443bd print msg to stderr; output more in fastmap Heng Li 2011-10-25 15:06:13 -0400
  • 7664795ffb fixed a minor issue about +/-1 Heng Li 2011-10-25 13:00:41 -0400
  • 7168f5c10a updated revision number Heng Li 2011-10-25 12:50:19 -0400
  • 4813257d4f remove debugging code Heng Li 2011-10-25 12:38:33 -0400
  • f56edd07dd forward-backward search seems working Heng Li 2011-10-25 12:31:36 -0400
  • aabb807734 concatenate for-rev sequences in the end Heng Li 2011-10-25 11:22:08 -0400
  • ca809a44d9 build .pac in memory; prepare for further changes Heng Li 2011-10-25 10:27:13 -0400
  • 7626595e3a backup the current debugging code; more changes Heng Li 2011-10-25 10:03:57 -0400
  • 22c2252e15 added bidirectional bwt; seems buggy Heng Li 2011-10-25 00:22:28 -0400
  • 7b4266a6e5 bugfix: integer overflow and strand error in sampe Heng Li 2011-10-24 17:07:12 -0400
  • b59fd2bf47 fixed an integer overflow Heng Li 2011-10-24 14:39:57 -0400
  • 8f3c780552 fixed a potential int overflow Heng Li 2011-10-24 14:22:39 -0400
  • 1f970b4557 updated revision number Heng Li 2011-10-24 14:14:42 -0400
  • eed46e802a fixed a bug about reverse alignment Heng Li 2011-10-24 14:09:05 -0400
  • b204437c7e fixed negative mapping quality; still byggy Heng Li 2011-10-24 14:00:36 -0400
  • 8512b55ce3 bwasw works on a couple of sequences Heng Li 2011-10-24 13:42:32 -0400
  • 4c43c5914d this is better; but still buggy Heng Li 2011-10-24 11:50:11 -0400
  • 29c3acfb31 not segfault immediately; but buggy Heng Li 2011-10-24 09:36:52 -0400
  • b3397a1f14 changes to bwa-sw for the 64-bit support; unfinish Heng Li 2011-10-21 13:32:45 -0400
  • 26b77eabef updated version number Heng Li 2011-10-21 12:32:00 -0400
  • 1cb409aaf2 use forward-only pac to reduce memory Heng Li 2011-10-21 12:03:14 -0400
  • fe9da3c704 allow to pac forward strand only Heng Li 2011-10-21 10:57:12 -0400
  • 66629512d9 more carefully computed the availableWords Heng Li 2011-10-20 23:49:03 -0400
  • ec307a10e6 PE seems working; more testing needed Heng Li 2011-10-20 17:45:41 -0400
  • 098f44cd51 nothing Heng Li 2011-10-20 16:26:14 -0400
  • 156852b1dd no change Heng Li 2011-10-20 16:15:16 -0400
  • 2d2db5d50f aln seems working Heng Li 2011-10-20 16:13:35 -0400
  • 46123639cf removed reverse pac; bwa is not working right now Heng Li 2011-10-20 12:09:35 -0400
  • b96f180a15 move bwt_gen/* to the root directory Heng Li 2011-10-20 11:56:24 -0400
  • 70da24e177 restructure bns_fasta2bntseq() for further changes Heng Li 2011-10-20 11:53:44 -0400
  • b7e8c4c5aa fixed a bug in 2occ4() Heng Li 2011-10-20 11:23:23 -0400
  • d6155ecf90 fixed a couple of gcc warnings Heng Li 2011-10-19 17:45:27 -0400
  • c948c647a0 make changes to bwt.c Heng Li 2011-10-19 17:42:42 -0400
  • b6d807b0b7 minor changes in case something goes wrong Heng Li 2011-10-19 13:50:50 -0400
  • 1f02acbe09 added a few assertions Heng Li 2011-10-19 00:26:56 -0400
  • 573ad0c98f merge bwt_gen.h to bwt_gen.c Heng Li 2011-10-18 23:48:46 -0400
  • 95b1ab7e96 first attempt to make bwt_gen work for >4GB seq Heng Li 2011-10-18 23:41:26 -0400
  • 3114edcb7c further code clean up Heng Li 2011-10-18 16:41:44 -0400
  • d2f357af3a a little bit code clean up Heng Li 2011-10-18 16:39:18 -0400
  • d70754e234 update revision number Heng Li 2011-10-14 10:32:31 -0400
  • 80e02281d5 minor change Heng Li 2011-10-14 10:31:48 -0400
  • 2255c4cd4b fixed a long existing bug Heng Li 2011-10-12 00:05:01 -0400
  • beedc988f0 Merge pull request #5 from tobiasmarschall/master Heng Li 2011-09-07 05:55:39 -0700
  • 3536e2113c Bugfix: reverse (complement) sequence and phred string if alternative alignment has different orientation than primary alignment Tobias Marschall 2011-09-07 14:31:28 +0200
  • 4f7734eb97 Merge pull request #2 from RoelKluin/master Heng Li 2011-07-10 12:27:55 -0700
  • db59a605d1 Remove sequences marked to be filtered by Casava-1.8 with bwa aln -Y Roel Kluin 2011-07-10 17:04:06 +0200
  • 8f115a8e00 Revert "In Casava 1.8 the fastq output changed, the name had a space which bwa" Roel Kluin 2011-07-10 16:40:42 +0200
  • 36cd4f9882 In Casava 1.8 the fastq output changed, the name had a space which bwa wasn't parsing correctly. This patch fixes that and enables bwa to filter sequences marked by Casava, removing this tag from the output. RoelKluin 2011-07-08 16:49:09 +0200
  • d11674367d convert XA to multiple lines Heng Li 2011-06-09 18:08:49 -0400
  • 72563c38f3 automatically choose the algorithm for BWT Heng Li 2011-06-09 17:33:25 -0400
  • a74523a68d increase maximum barcode length limit to 63bp Heng Li 2011-06-09 17:17:13 -0400
  • 243e735431 applied patches from Alec Wysoker Heng Li 2011-05-04 09:46:50 -0400
  • 4d064c69ce added -s to ar Heng Li 2011-05-04 09:41:30 -0400
  • 8d6b859bf8 speed up multi-threading Heng Li 2011-04-07 17:26:08 -0400
  • 87664941b0 Release bwa-0.5.9 (r16) Heng Li 2011-01-24 22:00:24 -0500
  • 7fd8948689 Added recommendation for PacBio reads Heng Li 2011-01-22 13:20:11 -0500
  • dac5395126 fixed a typo in help Heng Li 2011-01-21 23:56:18 -0500
  • 0380cf02bf update the manual page Heng Li 2011-01-18 23:27:55 -0500
  • 1d7d8be9e8 Put BC: to both ends Heng Li 2011-01-18 20:16:57 -0500
  • 51d354cd28 Added barcode support Heng Li 2011-01-15 15:35:39 -0500
  • 10721ca602 Added an option to accept Illumina 1.3+ fastq Heng Li 2011-01-15 14:07:08 -0500
  • f335b33624 fixed a bug in bwase: no RG for unmapped read pairs Heng Li 2011-01-15 10:32:45 -0500
  • 5b362b8718 Updated README Heng Li 2011-01-13 21:38:37 -0500
  • f85533c3c7 Updated README Heng Li 2011-01-13 21:28:26 -0500
  • ac93bbc6e4 Provided links to help information Heng Li 2011-01-13 21:19:02 -0500
  • 94122ad6ee Added a few others to .gitignore Heng Li 2011-01-13 21:14:00 -0500
  • fbedf6370b Added .gitignore Heng Li 2011-01-13 21:12:42 -0500
  • 5e30884730 Update to the latest modfication 0.5.9rc1-2. Update ChangeLog Heng Li 2011-01-13 20:54:10 -0500