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  • cb56fb762a Merge branch 'master' of github.com:lh3/minimap2 Heng Li 2020-03-22 19:17:01 -0400
  • e2451e497a r975: asmstat without CIGAR/NM Heng Li 2020-03-22 19:16:43 -0400
  • d2de282d21 remove second definition of kstring Jared Simpson 2020-03-02 12:44:08 -0500
  • 48cb80ea94 change kstring_t integer storage size Jared Simpson 2020-02-19 09:35:49 -0500
  • 6a4b9f9082 r974: more informative msg on wrong FASTQ records Heng Li 2020-01-21 10:56:59 -0500
  • a7a01fe5bd r973: fixed compiling errors caused Heng Li 2020-01-21 10:43:31 -0500
  • 9dceae59a0 r972: renamed --alt-diff to --alt-drop Heng Li 2020-01-21 10:33:39 -0500
  • 20a3987082 Merge branch 'master' into alt Heng Li 2020-01-21 09:16:45 -0500
  • eb3ed6993d support ALT mapping Heng Li 2020-01-20 19:32:31 -0500
  • 7996f04008 r972: fixed negative de:f caused by ambiguous base Heng Li 2020-01-21 09:14:37 -0500
  • d2e14705e7 r968: allow large mini_batch; resolves #491 Heng Li 2020-01-18 12:24:44 -0500
  • 24f50f38e8 r967: no duplicated @SQ lines with --split-prefix Heng Li 2020-01-18 12:01:28 -0500
  • 04e015d803 r966: minimap2 returns 1 on file failure (#532) Heng Li 2020-01-18 10:58:59 -0500
  • 040f74102c r965: added --chain-gap-scale for #540 Heng Li 2020-01-18 10:29:33 -0500
  • cdb7857841 r963: --junc-bonus not working; resolves #513 Heng Li 2020-01-06 22:03:50 -0500
  • 3c0d05d272 r962: abort given wrong RG line; resolves #541 Heng Li 2020-01-06 21:53:21 -0500
  • 47b646acbf r961: print indexed length Heng Li 2020-01-06 21:13:33 -0500
  • a79cb3e991 Merge remote-tracking branch 'origin/master' Heng Li 2019-12-23 17:33:56 -0500
  • 367aed4271 added the asan and tsan targets to Makefile Heng Li 2019-12-23 17:33:10 -0500
  • 081df6ac7d Fix example.c seq read logic xdudiagnoa 2019-09-16 17:21:40 +0800
  • a3e7a575fb Add splice:hq to --help Torsten Seemann 2019-11-04 07:38:10 +1100
  • d90583b83c r954: fixed two potential undef behaviors (#443) Heng Li 2019-07-18 09:17:08 -0400
  • 7fc03b0c32 r953: krealloc is buggy Heng Li 2019-07-18 09:13:30 -0400
  • 20c104ce8d Report errno on file opening failures and I/O errors John Marshall 2019-07-17 11:43:54 +0100
  • 238b6bb3ea Fix memory leak in mappy.aligner.map. Marcus Stoiber 2019-07-05 12:23:53 -0700
  • e026e18439 added the description of "SA" tag. Closes #438 Heng Li 2019-07-01 09:18:33 -0400
  • 58c2251b18 compatibility with GenBank GTP (resolves $422) Heng Li 2019-06-11 09:16:03 -0400
  • 03dc8d5d97 test if index is built for #413 Heng Li 2019-06-07 09:11:11 -0400
  • 5cb61f8ee6 added FAQ Heng Li 2019-06-06 10:47:33 -0400
  • c16a1742a3 Er... Tavis doesn't have python 3.7. Heng Li 2019-05-11 20:06:48 -0400
  • 4bd5a018c2 test python 3.7 instead of 3.6 Heng Li 2019-05-11 20:05:06 -0400
  • 05974c80f1 r943: allow long ref name for --split-index Heng Li 2019-05-10 15:39:41 -0400
  • 7bc87b4175 Release minimap2-2.17 (r941) Heng Li 2019-05-04 23:49:17 -0400
  • 6762368cf0 r940: added the splice:hq preset Heng Li 2019-05-04 14:00:31 -0400
  • c2aec88b84 r938: added --sam-hit-only; resolved #377 Heng Li 2019-04-30 22:40:36 -0400
  • 97f67a2a0a r937: enlarge mm_mapopt_t::flag to 64 bits Heng Li 2019-04-30 22:30:32 -0400
  • 189555503a potentially fix issue #372 Heng Li 2019-04-30 21:49:51 -0400
  • 69af86657e r935: fixed a cigar like 5I6D7I; resolved #392 Heng Li 2019-04-30 21:35:24 -0400
  • 49c6d83a8e r934: --junc-bed to read BED12 Heng Li 2019-04-28 20:12:28 -0400
  • f64e426a5a r933: resume versioning Heng Li 2019-04-28 17:05:37 -0400
  • 2bb8cbbeef updated manpage Heng Li 2019-04-28 17:02:49 -0400
  • e80759c97a --junc-bed apparently working Heng Li 2019-04-28 16:44:30 -0400
  • f4c844b143 fixed a few simple bugs and leaks Heng Li 2019-04-28 14:52:47 -0400
  • be171aa2dc implemented in exts; testing is the next Heng Li 2019-04-27 22:39:26 -0400
  • cdc730d573 gff2bed to output junction BED Heng Li 2019-04-27 22:15:40 -0400
  • 6420acca6d BED I/O Heng Li 2019-04-27 21:50:02 -0400
  • 371bc9513a SAM TLEN should be 0 when either read is unmapped John Marshall 2019-04-04 11:14:07 +0100
  • 169216bfff manpage was wrongly marked as "dirty" Heng Li 2019-02-28 15:58:12 -0500
  • 6b391e3373 Release minimap2-2.16 (r922) Heng Li 2019-02-28 15:49:24 -0500
  • 55e39c2d30 r921: output unmapped reads in full PAF Heng Li 2019-02-27 15:03:19 -0500
  • 90b7b83ec7 fix typo in command line help Kevin Chan 2018-12-18 17:52:20 -0800
  • d431dc0181 r917: added --max-chain-iter to avoid worst case Heng Li 2019-02-27 14:41:01 -0500
  • ccf1680aaf make it explicit that -x is preferred for prebuilt Heng Li 2019-02-27 12:43:33 -0500
  • ea84fc0a53 r917: fixed a bug in command-line parsing Heng Li 2019-02-27 11:21:57 -0500
  • 19208fb06b r916: support long cs in sam-to-paf conversion Heng Li 2019-02-17 09:35:23 -0500
  • e02bebd96d r915: fixed a bug caused by the latest change Heng Li 2019-02-14 10:04:04 -0500
  • 32ab6ce15b r914: fixed two harmless division by 0 Heng Li 2019-02-12 19:30:49 -0500
  • 1739a260fb r913: output tag "rl", length of unseedable regs Heng Li 2019-02-05 14:19:17 -0500
  • aaf3233818 added mappy.Aligner.seq_names to return seq names Heng Li 2019-01-29 12:53:20 -0500
  • 8b05880f73 r911: option -o to output to file (#319) Heng Li 2019-01-29 10:42:20 -0500
  • eba237f39d r910: meaningful error message (#320) Heng Li 2019-01-29 09:20:23 -0500
  • a8e1e3cbb8 updated citation with page numbers Heng Li 2019-01-26 17:59:36 -0500
  • 597212b9f3 r908: added an assertion to detect a potential bug Heng Li 2019-01-23 11:18:50 -0500
  • 30abcf3cf9 r907: copy tag "cs" in sam2paf Heng Li 2019-01-13 17:52:31 -0500
  • 48e230f40d r906: de tag is wrongly calculated given "N" Heng Li 2019-01-11 19:39:09 -0500
  • c404f49569 Release minimap2-2.15 (r905) Heng Li 2019-01-10 12:34:45 -0500
  • cf2bae6e9b r904: fixed a corner-case segfault. Resolves #307. Heng Li 2019-01-10 09:57:05 -0500
  • 5b2fdfff9c r895: option in asmgene to count autosomal only Heng Li 2018-12-14 10:36:47 -0500
  • ea2b1c5b2a r894: added --max-qlen to filter out long query Heng Li 2018-12-12 12:27:32 -0500
  • eef1cee9b7 r893: added paftools.js vcfpair Heng Li 2018-12-01 18:53:03 -0500
  • 2c52364527 r892: avoid de:f:0.0000 Heng Li 2018-11-24 21:54:28 -0500
  • 128476efc9 r891: compute gap-compressed divergence Heng Li 2018-11-24 21:50:49 -0500
  • 1b3a6a0fe5 r890: removed "register" (#261) Heng Li 2018-11-19 13:57:31 -0500
  • 83a8ee7038 r888: fixed incorrect CIGAR when --eqx in use Heng Li 2018-11-18 14:22:29 -0500
  • 62bbadf668 r887: fixed a bug in asmgene Heng Li 2018-11-11 21:35:19 -0500
  • 91f548b497 r886: fixed two minor typos Heng Li 2018-11-08 12:04:14 -0500
  • cdaf46665a r885: compute dup with asmstat Heng Li 2018-11-07 00:26:05 -0500
  • 6596c63dcd r884: for C++ compatibility (#261) Heng Li 2018-11-06 22:07:11 -0500
  • 59f23f7579 Release minimap2-2.14 (r883) Heng Li 2018-11-06 00:03:16 -0500
  • 5e55e397e9 r882: guard against -E0 (#263) Heng Li 2018-11-05 23:36:12 -0500
  • 88c421e8de r881: a recent change reduces sr accuracy Heng Li 2018-11-05 22:03:59 -0500
  • 3db5bfe6e5 r880: fixed false wrong FASTA/Q alert Heng Li 2018-11-05 20:52:07 -0500
  • 83dfdd5f50 draft release note Heng Li 2018-11-05 20:07:57 -0500
  • 8a2b1cd4c9 updated mappy for extra option max_sw_mat Heng Li 2018-11-05 19:28:44 -0500
  • 1ede8ca170 r877: renamed cap-sw-mat to cap-sw-mem Heng Li 2018-11-05 11:46:38 -0500
  • 13981404e2 r876: skip DP if taking too much RAM (#259) Heng Li 2018-11-05 11:43:10 -0500
  • fd64dd26f6 r875: warn given incorrect FASTA/Q Heng Li 2018-11-05 10:02:44 -0500
  • 24df95e4b8 r874: don't call x86_simd() so often Heng Li 2018-11-05 09:20:35 -0500
  • a8ee48c2ce r873: comforming to C99/C11; resolves #261 Heng Li 2018-11-05 08:25:07 -0500
  • 09e089c3dc r872: choose the longest isoform Heng Li 2018-11-04 23:48:50 -0500
  • e46cbb7d84 r871: print erroneous genes Heng Li 2018-11-04 20:37:06 -0500
  • 57ec73ec6c r870: separate <50% and <10% Heng Li 2018-11-04 19:31:25 -0500
  • 9e27575387 r869: classify incomplete genes Heng Li 2018-11-04 19:21:55 -0500
  • b4ad8d8bf0 added asmgene Heng Li 2018-11-04 17:24:05 -0500
  • e315b9fada hidden options to control bp calculation Heng Li 2018-11-04 16:36:04 -0500
  • 42baf287a4 r866: fixed a typo; resolves #262 Heng Li 2018-10-30 09:11:55 -0400
  • 2ceba22a7a fixed a typo in manpage Heng Li 2018-10-28 11:51:02 -0400
  • 9ed56b4a25 r860: MD/cs not working with --eqx Heng Li 2018-10-26 23:23:53 -0400
  • ecb6c5c36c Document --no-pairing (#256) Heng Li 2018-10-23 10:00:21 -0400
  • 377c7099a8 r858: fixed a bug; resolves #254 Heng Li 2018-10-22 22:47:11 -0400