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Commit Graph

  • 5dcd8f8965 r117: fixed a bug in logic Heng Li 2017-06-30 11:52:42 -04:00
  • 91e1c4d6db r116: fixed another bug caused by refactoring Heng Li 2017-06-30 00:03:45 -04:00
  • 52b4d8e2c9 r115: set primary tag; still buggy Heng Li 2017-06-29 23:48:35 -04:00
  • c4871f380c r114: make SAM output better Heng Li 2017-06-29 23:08:41 -04:00
  • 03267e8fa7 r113: fixed a sam header bug Heng Li 2017-06-29 22:43:06 -04:00
  • 11167f511b r112: output z-drop Heng Li 2017-06-29 22:08:46 -04:00
  • 3825feeeac r111: changed the default z-drop to 200 Heng Li 2017-06-29 21:37:56 -04:00
  • e2b86d0332 r110: fixed a bug caused by refactoring Heng Li 2017-06-29 21:12:31 -04:00
  • 08cbb09fcc r109: changed the default scoring Heng Li 2017-06-29 20:21:57 -04:00
  • 4cd456b9ba r108: refactoring, move reg1 routines to hit.c Heng Li 2017-06-29 19:44:11 -04:00
  • ecedfe5788 code refactoring for mm_reg1_t Heng Li 2017-06-29 19:35:38 -04:00
  • cc67f1b781 compute mapq; not working for z-split yet Heng Li 2017-06-29 17:52:48 -04:00
  • 337c2a21cd r105: fixed a bug in repeated right ext when zdrop Heng Li 2017-06-29 15:45:07 -04:00
  • b9075d39a8 r104: long gap patching Heng Li 2017-06-29 14:54:54 -04:00
  • 17944a75c2 merge into map.c Heng Li 2017-06-29 14:20:14 -04:00
  • d274e1b743 backup Heng Li 2017-06-29 12:58:52 -04:00
  • c8d122bcdb backup Heng Li 2017-06-29 11:11:15 -04:00
  • 9fbf7e41e1 r99: report progress Heng Li 2017-06-28 23:56:33 -04:00
  • cf703655cb optional sse4 Heng Li 2017-06-28 22:21:52 -04:00
  • 38070e8a05 r98: fixed segfault for certain scoring Heng Li 2017-06-28 22:18:51 -04:00
  • 5e202afb5f fixed invalid backtracking, a temporary solution Heng Li 2017-06-28 18:17:57 -04:00
  • a25866c25c r96: min_cnt still wrong in chaining Heng Li 2017-06-28 11:03:03 -04:00
  • b696d5fe5e disable kalloc in the debugging mode Heng Li 2017-06-28 10:50:27 -04:00
  • bf0e8199e2 r94: min_cnt is tested in a wrong way in chain Heng Li 2017-06-28 10:39:27 -04:00
  • bcd9b1c621 r93: fixed various small issues Heng Li 2017-06-28 10:35:21 -04:00
  • cdc2a1e29f r92: fixed a bug for overlapping alignment Heng Li 2017-06-27 22:03:31 -04:00
  • 51057ab673 expose scoring Heng Li 2017-06-27 21:37:25 -04:00
  • 533150d49d r90: revert default band width to 1000 Heng Li 2017-06-27 20:29:39 -04:00
  • fa80177e58 r89: added minimal number of minimizer counts Heng Li 2017-06-27 18:43:15 -04:00
  • 8977f07269 r88: fixed an out-of-boundary bug in ksw2 Heng Li 2017-06-27 14:50:31 -04:00
  • 42283ef10c r87: fixed a bug in ksw2 Heng Li 2017-06-27 13:29:48 -04:00
  • 734028f92b validate z-drop Heng Li 2017-06-27 11:25:39 -04:00
  • c02ff4662c r85: two-round z-drop Heng Li 2017-06-27 10:36:24 -04:00
  • 490a37a599 number of allocated units must be an even number Heng Li 2017-06-26 23:15:30 -04:00
  • 0d03a43efd don't round to power-of-2 Heng Li 2017-06-26 22:10:45 -04:00
  • b56cd790f6 enabled kalloc (was a mistake) Heng Li 2017-06-26 15:41:55 -04:00
  • 99c57b86c5 r79: drop bad hits Heng Li 2017-06-26 15:28:04 -04:00
  • 5b614ae828 r78: fixed a split bug Heng Li 2017-06-26 14:45:23 -04:00
  • de54c9dac2 r77: fixed an index loading bug (offset not set) Heng Li 2017-06-26 13:56:25 -04:00
  • 10644f2165 r76: missing header file Heng Li 2017-06-26 12:36:37 -04:00
  • 4b8e88a5f4 use long options Heng Li 2017-06-26 12:31:36 -04:00
  • 640b1a1727 command-line option to control CIGAR output Heng Li 2017-06-26 11:41:09 -04:00
  • 24d7f7f8b1 disabled dynamic banding; buggy Heng Li 2017-06-25 22:43:15 -04:00
  • b1077ff14c sam output Heng Li 2017-06-25 22:05:20 -04:00
  • 39083be9ab separated formating printing Heng Li 2017-06-25 16:13:54 -04:00
  • 7780ab792a removed some comment lines Heng Li 2017-06-25 11:53:35 -04:00
  • 56364200c8 avoid contained hits due to split Heng Li 2017-06-25 11:43:50 -04:00
  • f20d550a59 fixed the NM bug Heng Li 2017-06-25 11:24:39 -04:00
  • b261a4a74b zdrop sort of works, but has issues Heng Li 2017-06-25 10:52:14 -04:00
  • 72dfb0c99e fixed a bug in ksw2 Heng Li 2017-06-25 10:22:13 -04:00
  • ef5dd318ca implemented chain splitting; NOT tested!!! Heng Li 2017-06-24 22:57:43 -04:00
  • aa5881e7bb backup Heng Li 2017-06-24 22:51:31 -04:00
  • d08b58d21f minor Heng Li 2017-06-24 19:33:59 -04:00
  • 672782f03a simplified hp_len a little Heng Li 2017-06-24 19:27:58 -04:00
  • 2d8fda9586 an alternative strategy to fix for HPC Heng Li 2017-06-24 09:26:24 -04:00
  • 6088dc11ff wrong SW score Heng Li 2017-06-23 23:24:49 -04:00
  • 0c274280ae output the original score Heng Li 2017-06-23 22:56:50 -04:00
  • 2987be288c output cigar Heng Li 2017-06-23 22:53:47 -04:00
  • 35b84f88c6 backup Heng Li 2017-06-23 22:42:15 -04:00
  • 523a8832ad backup Heng Li 2017-06-23 20:57:17 -04:00
  • 7ed26a4857 backup Heng Li 2017-06-23 19:31:23 -04:00
  • d75b5b4e8a backup; NOT working yet Heng Li 2017-06-23 19:21:47 -04:00
  • 4fea3d778a backup Heng Li 2017-06-23 18:57:00 -04:00
  • 6c8368c24c get the left-extension sequence correctly Heng Li 2017-06-23 18:25:47 -04:00
  • 990f7b0b71 backup Heng Li 2017-06-23 15:13:53 -04:00
  • 4ae0b46972 min_ksw_len Heng Li 2017-06-23 14:38:28 -04:00
  • 9cd313eae1 sequence retrieval working Heng Li 2017-06-23 14:11:56 -04:00
  • 326d91deb0 backup Heng Li 2017-06-23 14:06:00 -04:00
  • 44cdd18de0 start to work on alignment Heng Li 2017-06-23 13:44:45 -04:00
  • c6d5dea314 replace with newer versions Heng Li 2017-06-22 12:30:45 -04:00
  • fbfd4a3eff to replace Heng Li 2017-06-22 12:30:22 -04:00
  • 8e0d73740e moved aln-dp.tex to ksw2/tex (a new repo) Heng Li 2017-06-18 11:21:34 -04:00
  • fe8327500f implemented SSE version; NOT working yet Heng Li 2017-06-16 21:35:51 -04:00
  • 359b829350 fixed a boundary bug in global() Heng Li 2017-06-16 12:47:09 -04:00
  • 7d33acbccc diagonal global almost working Heng Li 2017-06-16 12:17:23 -04:00
  • c4564c31a2 explain DP Heng Li 2017-06-15 19:37:48 -04:00
  • 78fe89d1ab revert to fixed band Heng Li 2017-06-14 14:22:23 -04:00
  • d3f17b1e05 updated ksw Heng Li 2017-06-11 16:51:01 -04:00
  • 372698bb23 disable k-mer intersection for now Heng Li 2017-06-11 14:13:41 -04:00
  • b04e4b9215 r36: bring back primary; don't output all mappings Heng Li 2017-06-08 15:28:19 -04:00
  • 6c099bef89 removed some debugging code Heng Li 2017-06-07 14:49:11 -04:00
  • 19e43571c1 r34: removed a bit unused code Heng Li 2017-06-07 14:35:57 -04:00
  • be9a7f4e41 removed the old print code Heng Li 2017-06-07 14:24:31 -04:00
  • 8ad5cfde42 output PAF Heng Li 2017-06-07 14:18:32 -04:00
  • c01f2dd757 fixed a bug Heng Li 2017-06-07 11:40:13 -04:00
  • 77c76c1e14 fixed an integer overflow Heng Li 2017-06-06 22:20:45 -04:00
  • c1c946aa67 fixed memory leaks Heng Li 2017-06-06 21:45:55 -04:00
  • e6adb673f9 fixed a stupid bug Heng Li 2017-06-06 15:45:42 -04:00
  • a2958a4836 minor tweaks Heng Li 2017-06-06 15:31:21 -04:00
  • d816e48fce fixed a bug in chaining Heng Li 2017-06-06 14:33:43 -04:00
  • 6d4348db44 dp chaining mostly works, but fails sometimes Heng Li 2017-06-06 14:19:50 -04:00
  • 1a9fc04cf0 backup Heng Li 2017-06-06 10:16:33 -04:00
  • acc7382a30 backup Heng Li 2017-06-04 16:09:45 -04:00
  • 949d9be872 chaining with DP Heng Li 2017-05-09 22:20:57 +08:00
  • 2827c29b48 minor backup Heng Li 2017-05-04 23:22:11 +08:00
  • 10db6b0434 wrong HPC Heng Li 2017-05-04 17:45:19 +08:00
  • 06adabd0dc clean bill from valgrind Heng Li 2017-05-04 12:44:49 +08:00
  • 7b53f7aa84 chaining Heng Li 2017-05-03 20:47:29 +08:00
  • f2ae8eb670 mostly debugging code Heng Li 2017-05-01 16:50:09 +08:00
  • 2c9f1bce3e k-mer thinning apparently working Heng Li 2017-04-28 18:24:45 +08:00