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  • c2aec88b84 r938: added --sam-hit-only; resolved #377 Heng Li 2019-04-30 22:40:36 -04:00
  • 97f67a2a0a r937: enlarge mm_mapopt_t::flag to 64 bits Heng Li 2019-04-30 22:30:32 -04:00
  • 189555503a potentially fix issue #372 Heng Li 2019-04-30 21:49:51 -04:00
  • 69af86657e r935: fixed a cigar like 5I6D7I; resolved #392 Heng Li 2019-04-30 21:35:24 -04:00
  • 49c6d83a8e r934: --junc-bed to read BED12 Heng Li 2019-04-28 20:12:28 -04:00
  • f64e426a5a r933: resume versioning Heng Li 2019-04-28 17:05:37 -04:00
  • 2bb8cbbeef updated manpage Heng Li 2019-04-28 17:02:49 -04:00
  • e80759c97a --junc-bed apparently working Heng Li 2019-04-28 16:44:30 -04:00
  • f4c844b143 fixed a few simple bugs and leaks Heng Li 2019-04-28 14:52:47 -04:00
  • be171aa2dc implemented in exts; testing is the next Heng Li 2019-04-27 22:39:26 -04:00
  • cdc730d573 gff2bed to output junction BED Heng Li 2019-04-27 22:15:40 -04:00
  • 6420acca6d BED I/O Heng Li 2019-04-27 21:50:02 -04:00
  • 371bc9513a SAM TLEN should be 0 when either read is unmapped John Marshall 2019-04-04 11:14:07 +01:00
  • e9a45a4e1c Merge branch 'master' into avx Heng Li 2019-03-04 11:15:56 -05:00
  • 514612bda2 updated manpage to v2.16 Heng Li 2019-02-28 15:59:13 -05:00
  • 169216bfff manpage was wrongly marked as "dirty" Heng Li 2019-02-28 15:58:12 -05:00
  • 6b391e3373 Release minimap2-2.16 (r922) v2.16 Heng Li 2019-02-28 15:49:24 -05:00
  • 55e39c2d30 r921: output unmapped reads in full PAF Heng Li 2019-02-27 15:03:19 -05:00
  • 90b7b83ec7 fix typo in command line help Kevin Chan 2018-12-18 17:52:20 -08:00
  • d431dc0181 r917: added --max-chain-iter to avoid worst case Heng Li 2019-02-27 14:41:01 -05:00
  • ccf1680aaf make it explicit that -x is preferred for prebuilt Heng Li 2019-02-27 12:43:33 -05:00
  • ea84fc0a53 r917: fixed a bug in command-line parsing Heng Li 2019-02-27 11:21:57 -05:00
  • 19208fb06b r916: support long cs in sam-to-paf conversion Heng Li 2019-02-17 09:35:23 -05:00
  • e02bebd96d r915: fixed a bug caused by the latest change Heng Li 2019-02-14 10:04:04 -05:00
  • 32ab6ce15b r914: fixed two harmless division by 0 Heng Li 2019-02-12 19:30:49 -05:00
  • 1739a260fb r913: output tag "rl", length of unseedable regs Heng Li 2019-02-05 14:19:17 -05:00
  • aaf3233818 added mappy.Aligner.seq_names to return seq names Heng Li 2019-01-29 12:53:20 -05:00
  • 8b05880f73 r911: option -o to output to file (#319) Heng Li 2019-01-29 10:42:20 -05:00
  • eba237f39d r910: meaningful error message (#320) Heng Li 2019-01-29 09:20:23 -05:00
  • a8e1e3cbb8 updated citation with page numbers Heng Li 2019-01-26 17:59:36 -05:00
  • 597212b9f3 r908: added an assertion to detect a potential bug Heng Li 2019-01-23 11:18:50 -05:00
  • 30abcf3cf9 r907: copy tag "cs" in sam2paf Heng Li 2019-01-13 17:52:31 -05:00
  • 48e230f40d r906: de tag is wrongly calculated given "N" Heng Li 2019-01-11 19:39:09 -05:00
  • c404f49569 Release minimap2-2.15 (r905) v2.15 Heng Li 2019-01-10 12:34:45 -05:00
  • cf2bae6e9b r904: fixed a corner-case segfault. Resolves #307. Heng Li 2019-01-10 09:57:05 -05:00
  • f5e2176bc5 r903: merged extd2_avx512.c into extd2_sse.c Heng Li 2019-01-01 13:46:30 -05:00
  • 0b4be2996e avx512 working on MT Heng Li 2019-01-01 13:05:30 -05:00
  • feca68c71d fixed two bugs when computing full score Heng Li 2019-01-01 11:46:01 -05:00
  • 6d9ce56721 blend was reversed Heng Li 2019-01-01 10:27:59 -05:00
  • f2f425890d can be compiled on Linux Heng Li 2019-01-01 10:04:03 -05:00
  • 58f4210dea compiled, but not working Heng Li 2019-01-01 01:32:43 -05:00
  • a4782c7d7a r897: avx2 working on test/MT-*.fa Heng Li 2018-12-31 10:26:19 -05:00
  • 2a7d071e8b minor equivalent changes Heng Li 2018-12-30 23:15:07 -05:00
  • 9462da5159 initial avx2 support; not working properly yet Heng Li 2018-12-30 11:09:44 -05:00
  • 5b2fdfff9c r895: option in asmgene to count autosomal only Heng Li 2018-12-14 10:36:47 -05:00
  • ea2b1c5b2a r894: added --max-qlen to filter out long query Heng Li 2018-12-12 12:27:32 -05:00
  • eef1cee9b7 r893: added paftools.js vcfpair Heng Li 2018-12-01 18:53:03 -05:00
  • 2c52364527 r892: avoid de:f:0.0000 Heng Li 2018-11-24 21:54:28 -05:00
  • 128476efc9 r891: compute gap-compressed divergence Heng Li 2018-11-24 21:50:49 -05:00
  • 1b3a6a0fe5 r890: removed "register" (#261) Heng Li 2018-11-19 13:57:31 -05:00
  • 83a8ee7038 r888: fixed incorrect CIGAR when --eqx in use Heng Li 2018-11-18 14:22:29 -05:00
  • 62bbadf668 r887: fixed a bug in asmgene Heng Li 2018-11-11 21:35:19 -05:00
  • 91f548b497 r886: fixed two minor typos Heng Li 2018-11-08 12:04:14 -05:00
  • cdaf46665a r885: compute dup with asmstat Heng Li 2018-11-07 00:26:05 -05:00
  • 6596c63dcd r884: for C++ compatibility (#261) Heng Li 2018-11-06 22:07:11 -05:00
  • 59f23f7579 Release minimap2-2.14 (r883) v2.14 Heng Li 2018-11-06 00:03:16 -05:00
  • 5e55e397e9 r882: guard against -E0 (#263) Heng Li 2018-11-05 23:36:12 -05:00
  • 88c421e8de r881: a recent change reduces sr accuracy Heng Li 2018-11-05 22:03:59 -05:00
  • 3db5bfe6e5 r880: fixed false wrong FASTA/Q alert Heng Li 2018-11-05 20:52:07 -05:00
  • 83dfdd5f50 draft release note Heng Li 2018-11-05 20:07:57 -05:00
  • 8a2b1cd4c9 updated mappy for extra option max_sw_mat Heng Li 2018-11-05 19:28:44 -05:00
  • 1ede8ca170 r877: renamed cap-sw-mat to cap-sw-mem Heng Li 2018-11-05 11:46:38 -05:00
  • 13981404e2 r876: skip DP if taking too much RAM (#259) Heng Li 2018-11-05 11:43:10 -05:00
  • fd64dd26f6 r875: warn given incorrect FASTA/Q Heng Li 2018-11-05 10:02:44 -05:00
  • 24df95e4b8 r874: don't call x86_simd() so often Heng Li 2018-11-05 09:20:35 -05:00
  • a8ee48c2ce r873: comforming to C99/C11; resolves #261 Heng Li 2018-11-05 08:25:07 -05:00
  • 09e089c3dc r872: choose the longest isoform Heng Li 2018-11-04 23:48:50 -05:00
  • e46cbb7d84 r871: print erroneous genes Heng Li 2018-11-04 20:37:06 -05:00
  • 57ec73ec6c r870: separate <50% and <10% Heng Li 2018-11-04 19:31:25 -05:00
  • 9e27575387 r869: classify incomplete genes Heng Li 2018-11-04 19:21:55 -05:00
  • b4ad8d8bf0 added asmgene Heng Li 2018-11-04 17:24:05 -05:00
  • e315b9fada hidden options to control bp calculation Heng Li 2018-11-04 16:36:04 -05:00
  • 42baf287a4 r866: fixed a typo; resolves #262 Heng Li 2018-10-30 09:11:55 -04:00
  • e39080fea6 debugging code bed-bonus Heng Li 2018-10-29 19:50:31 -04:00
  • e9dcd7b2bc read score from BED Heng Li 2018-10-29 15:07:48 -04:00
  • 2ceba22a7a fixed a typo in manpage Heng Li 2018-10-28 11:51:02 -04:00
  • 9ed56b4a25 r860: MD/cs not working with --eqx Heng Li 2018-10-26 23:23:53 -04:00
  • ecb6c5c36c Document --no-pairing (#256) Heng Li 2018-10-23 10:00:21 -04:00
  • 377c7099a8 r858: fixed a bug; resolves #254 Heng Li 2018-10-22 22:47:11 -04:00
  • 51e2abfa60 clarify that minimap2 may miss small exons Heng Li 2018-10-22 11:16:16 -04:00
  • 7b0a49732e r856: wrongly reported for an unrecognized option Heng Li 2018-10-19 20:07:14 -04:00
  • 121731ebde Merge branch 'master' into bed-bonus Heng Li 2018-10-18 11:13:19 -04:00
  • 20268a6068 updated the copyright holder Heng Li 2018-10-18 11:11:17 -04:00
  • 0aad789ac4 updated copyright holder Heng Li 2018-10-18 11:10:47 -04:00
  • d04ac068fd r852: a minor when large --end-bonus is in use Heng Li 2018-10-15 21:28:27 -04:00
  • 3508ac9817 updated manpage to v2.13 Heng Li 2018-10-11 13:35:09 -04:00
  • 5d5d392c02 Release minimap2-2.13 (r850) v2.13 Heng Li 2018-10-11 13:18:31 -04:00
  • 170863e553 r849: option -P doesn't work Heng Li 2018-10-04 16:11:59 -04:00
  • 97f97306a4 r847: guard against -N0 Heng Li 2018-09-27 15:13:44 -04:00
  • 1077b7ddc8 r846: added --hard-mask-level for #244 Heng Li 2018-09-27 14:46:26 -04:00
  • c57b59f02f r845: log peak memory Heng Li 2018-09-23 20:27:49 -04:00
  • 34be359e25 Add -s sample option for VCF output Torsten Seemann 2018-09-19 14:54:37 -04:00
  • 2d065eea7e fixed a BED parsing bug Heng Li 2018-09-17 15:50:28 -04:00
  • b4b70db126 mappy to support BED Heng Li 2018-09-17 14:54:44 -04:00
  • a3e223f17b Merge branch 'master' into bed-prefer Heng Li 2018-09-17 13:59:51 -04:00
  • 8b12da8b0f removed a useless dependency (not in repo) Heng Li 2018-09-17 13:59:25 -04:00
  • edf736e110 working on toy examples Heng Li 2018-09-17 13:54:57 -04:00
  • d01369ec47 pass BED regions to extd2; not tested Heng Li 2018-09-17 12:31:42 -04:00
  • 2b653ecda3 BED I/O Heng Li 2018-09-16 14:49:53 -04:00
  • c63a33904f r836: fixed an integer overflow Heng Li 2018-09-14 23:29:31 -04:00