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Commit Graph

  • 5e3eecd6d4 r222: no effective changes Heng Li 2017-07-29 10:31:46 -04:00
  • 2179e9e24b r221: output SA in the SAM output Heng Li 2017-07-28 23:08:39 -04:00
  • 84922cfe41 clarify that wrong seeding mainly occurs in LCRs Heng Li 2017-07-28 14:33:15 -04:00
  • ebbe9c1eb8 r219: fixed a bug caused by skipping tandem seeds Heng Li 2017-07-28 14:06:56 -04:00
  • c672690564 r218: increase the frequency of SW slightly Heng Li 2017-07-28 13:30:42 -04:00
  • f4fee60188 r217: ignore tandem seeds during alignment Heng Li 2017-07-28 12:26:56 -04:00
  • 254280b8af r216: a bit cleanup; identical output to r215 Heng Li 2017-07-28 11:54:18 -04:00
  • fc965805f7 r215: bring back a log gap component Heng Li 2017-07-28 00:17:19 -04:00
  • 667b32a516 added algorithm overview Heng Li 2017-07-27 18:50:39 -04:00
  • 2c79580649 r213: more careful solution to wrong seeds Heng Li 2017-07-27 13:19:11 -04:00
  • b927838495 r212: better heuristic to fix wrong seeding Heng Li 2017-07-27 11:24:51 -04:00
  • 371e20cc7c r211: a better heurstic to reduce false seeds Heng Li 2017-07-26 23:56:38 -04:00
  • 8b08a2ec41 added first-only and all-primary modes to eval Heng Li 2017-07-26 19:32:26 -04:00
  • 9f728dd96a tunable overlap ratio Heng Li 2017-07-26 18:30:29 -04:00
  • 323293fbda changed the way mapq is counted Heng Li 2017-07-26 14:20:31 -04:00
  • bd33bed455 make output better Heng Li 2017-07-26 12:03:42 -04:00
  • a01d758af6 r206: mapq penalize short chains further Heng Li 2017-07-26 11:50:04 -04:00
  • e9dc1ce2b6 r205: when computing mapq, consider min_chain_sc Heng Li 2017-07-26 11:34:14 -04:00
  • a8ad53ee81 evaluating read mapping for pbsim2fa reads Heng Li 2017-07-26 11:17:34 -04:00
  • 00c6db5073 r203: check more subopt aln if score small Heng Li 2017-07-25 20:02:44 -04:00
  • f2ef48878a r202: trim bad chain ends before extension Heng Li 2017-07-25 19:53:19 -04:00
  • 21ca564112 r201: fixed a minor chaining issue Heng Li 2017-07-25 18:26:51 -04:00
  • 215e92ed7b r200: reduce long gaps in chaining Heng Li 2017-07-25 17:32:54 -04:00
  • b530ade333 r199: changed to linear gap cost for chaining Heng Li 2017-07-25 15:35:10 -04:00
  • 4bd7ebc39c convert pbsim .maf to fasta Heng Li 2017-07-25 13:54:58 -04:00
  • f81f37fef1 r197: allocate index seq names from kalloc Heng Li 2017-07-24 19:36:05 -04:00
  • 5c4d040b13 r191: warning if CLI index opt diff from prebuilt r191 Heng Li 2017-07-19 10:25:11 -04:00
  • 4aff301ef4 r190: default -k to 15; added -x map-ont Heng Li 2017-07-19 10:11:14 -04:00
  • 470021fd27 r189: sync with ksw2 (no effective changes) Heng Li 2017-07-19 09:28:25 -04:00
  • 71c988f6ab r188: renamed bseq* to mm_bseq* Heng Li 2017-07-19 09:26:46 -04:00
  • b9b0b6f49c r187: fixed non-terminated sam output (#3) Heng Li 2017-07-18 15:20:29 -04:00
  • 947cf162be update dependency; delete minimap2-lite on clean Heng Li 2017-07-18 14:48:46 -04:00
  • 293a7049f3 migrated minimap/example.c here. Heng Li 2017-07-18 14:43:43 -04:00
  • a1addb2949 use -msse4 by default, not -march Heng Li 2017-07-18 13:56:51 -04:00
  • b4edb0cf55 fixed URL Heng Li 2017-07-18 13:26:51 -04:00
  • 9a935dcef5 Fixed grammar errors Heng Li 2017-07-18 11:37:58 -04:00
  • 495a78e40a Get documentation ready for release Heng Li 2017-07-18 11:04:09 -04:00
  • 71e2a97a4c r180: changed -x asm5 settings Heng Li 2017-07-18 00:00:36 -04:00
  • 941059292e r179: changed the preset for assembly alignment Heng Li 2017-07-17 22:41:46 -04:00
  • 38aa66fa30 r178: fixed integer overflow in mapq calculation Heng Li 2017-07-16 21:45:39 -04:00
  • f42790398d fixed a band boundary bug in ksw2 Heng Li 2017-07-16 17:52:57 -04:00
  • b4280d186f r176: removed seedcov_ratio; changed default opt Heng Li 2017-07-12 12:47:46 -04:00
  • 52caf79395 r175: halved max-chain-skip in the ava mode Heng Li 2017-07-12 10:42:19 -04:00
  • eeeb2ffb68 r174: make max-chain-skip work Heng Li 2017-07-12 10:08:06 -04:00
  • 33451aba45 r173: changed the debugging output format Heng Li 2017-07-11 15:23:28 -04:00
  • cfa083a98b r172: separated PacBio and ONT read overlapping Heng Li 2017-07-11 15:12:35 -04:00
  • 7598809577 r171: reduced log gap cost at chaining Heng Li 2017-07-11 14:57:49 -04:00
  • 826c8ba892 r170: added a debugging flag Heng Li 2017-07-11 14:47:35 -04:00
  • 801bc84b01 r169: output more accurate col. 10&11 to PAF Heng Li 2017-07-11 14:09:51 -04:00
  • 782449975d r168: fixed a bug in long join: a[] not sorted Heng Li 2017-07-09 12:14:20 -04:00
  • 1ac48556ae r167: long join threshold depends on gap Heng Li 2017-07-09 10:38:51 -04:00
  • 34ed85d46a optionally print the postions of long indels Heng Li 2017-07-08 20:16:25 -04:00
  • 2f11a63b22 script to collect alignment stats Heng Li 2017-07-08 20:01:36 -04:00
  • 4ee3202539 r164: unmapped read not properly flagged Heng Li 2017-07-08 18:16:18 -04:00
  • 42846ce65d r163: reduced long join score requirement Heng Li 2017-07-08 15:51:52 -04:00
  • 3f6a0b0b5c r162: improved chaining accuracy Heng Li 2017-07-08 14:29:36 -04:00
  • 38b2830e18 r161: filter bad seeds; changed default -g/-r Heng Li 2017-07-08 13:31:27 -04:00
  • 1fee5f8edc r160: -O and -E accept two numbers Heng Li 2017-07-08 11:34:52 -04:00
  • cc554aee43 r159: use two-piece gap penalty Heng Li 2017-07-08 10:26:00 -04:00
  • 9823317e8f r158: optionally ignore base quality Heng Li 2017-07-05 18:23:50 -04:00
  • d1f518e3ca for clarity Heng Li 2017-07-04 11:56:50 -04:00
  • 6b584a1235 added README Heng Li 2017-07-04 11:47:29 -04:00
  • 8fff901e53 added test data Heng Li 2017-07-04 10:56:48 -04:00
  • a65e557a7c Merge branch 'dev' Heng Li 2017-07-03 13:19:17 -04:00
  • e07daad7ad r153: sam primary record not set sometimes Heng Li 2017-07-03 13:18:57 -04:00
  • 6ead8af104 Merge branch 'dev' into 'master' Heng Li 2017-07-03 16:17:08 +00:00
  • a94bc31311 r151: documentations Heng Li 2017-07-03 12:11:07 -04:00
  • b625247300 r150: mm_sync_regs() doesn't work with negative id Heng Li 2017-07-03 11:36:34 -04:00
  • 53c4bf5e4f r149: introduced debugging flags on CLI Heng Li 2017-07-03 11:02:32 -04:00
  • 2e4fd9f1d0 r148: revamped regs handling after cigar Heng Li 2017-07-03 10:44:26 -04:00
  • 696ebce66e backup; still buggy Heng Li 2017-07-03 00:52:00 -04:00
  • e06c342659 r146: in filtering, drop children if parent out Heng Li 2017-07-03 00:28:12 -04:00
  • 51cfb60520 r145: changed default -p from 2 to 0.8 Heng Li 2017-07-02 22:51:45 -04:00
  • 632b8638d2 r144: adjust primary aln after cigar Heng Li 2017-07-02 22:43:02 -04:00
  • 2b45ba7a0b r143: fixed a segfault and incorrect .parent Heng Li 2017-07-02 19:56:21 -04:00
  • 74d306a596 fixed bug when retaining 2ndary aln; still buggy Heng Li 2017-07-02 19:08:30 -04:00
  • da90b614db r141: replaced -b with -a (for SAM output) Heng Li 2017-07-01 16:54:59 -04:00
  • 67cad9dff3 added limitations Heng Li 2017-07-01 12:11:56 -04:00
  • a92bd75b7b make the table fit 80 columns Heng Li 2017-07-01 11:54:07 -04:00
  • 02145b2166 explain option -d Heng Li 2017-07-01 11:48:37 -04:00
  • 3c45d84012 added license Heng Li 2017-07-01 11:39:19 -04:00
  • b2ce3f9ed0 get rid of two more new lines Heng Li 2017-07-01 11:37:58 -04:00
  • 5ebe868db5 added two more new lines Heng Li 2017-07-01 11:32:49 -04:00
  • cb6c277c62 removed unnecessary empty lines Heng Li 2017-07-01 11:31:32 -04:00
  • b883d132e2 no effective change Heng Li 2017-07-01 11:26:23 -04:00
  • 2338e887d9 finished the first draft of manpage Heng Li 2017-07-01 11:25:54 -04:00
  • a9f089f0aa r131: wrong EOF test; make mb_size <= batch_size Heng Li 2017-07-01 09:26:09 -04:00
  • d4301736b8 more manpage Heng Li 2017-07-01 00:23:46 -04:00
  • 41efd03d7a r129: fixed memory leak caused by qualities Heng Li 2017-06-30 23:48:00 -04:00
  • 10910b72d1 backup Heng Li 2017-06-30 23:31:38 -04:00
  • d118cafd25 added man page Heng Li 2017-06-30 23:30:17 -04:00
  • 426c2975f6 r126: filter by fraction of seed coverage Heng Li 2017-06-30 22:15:45 -04:00
  • d73bb28097 r125: changed CLI options Heng Li 2017-06-30 19:08:47 -04:00
  • b08591c7a0 r124: a bit better CLI prompt Heng Li 2017-06-30 15:46:52 -04:00
  • 3a5486325a r123: fixed a mem leak; more presets Heng Li 2017-06-30 15:39:05 -04:00
  • 646a746cdc r122: filter contained aln after DP extension Heng Li 2017-06-30 15:23:30 -04:00
  • fce87ce7bd r121: output QUAL and unmapped to SAM Heng Li 2017-06-30 14:40:54 -04:00
  • d11049eb32 r120: use max-scoring seg to control output Heng Li 2017-06-30 14:21:44 -04:00
  • 08a61c3cfc r119: fixed a bug hidden by a previous bug Heng Li 2017-06-30 13:27:47 -04:00
  • 1a903486b9 r118: bugfix - regs unsorted before filtering Heng Li 2017-06-30 12:52:28 -04:00