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• 42a11e1d58 Changed Travis to Github Actions in README Heng Li 2021-05-10 12:58:25 -04:00
• 76df351fa8 added github action Heng Li 2021-05-10 12:55:58 -04:00
• d065d3bead Merge branch 'master' into dev-rmq Heng Li 2021-05-10 12:42:57 -04:00
• ac146fe7bc r1035: failed to index under the --frag=yes mode Heng Li 2021-05-10 12:36:48 -04:00
• 6c96078ed0 r1034: changed multiple defaults; updated manpage Heng Li 2021-05-03 22:51:34 -04:00
• bbb4f97e52 support RMQ Heng Li 2021-05-03 09:27:04 -04:00
• b7f4d8a0f4 removed the old minimap2 chaining Heng Li 2021-05-02 18:55:37 -04:00
• e81927e7a1 prepare to backport unimap/minigraph chaining Heng Li 2021-05-02 18:25:49 -04:00
• f7dc5799c5 clarify CLR when necessary Heng Li 2021-05-01 15:56:33 -04:00
• 817cb81cb0 Updated README for the HiFi preset Heng Li 2021-05-01 15:47:25 -04:00
• 0f5608c4a4 r1028: backport minigraph -U Heng Li 2021-05-01 15:41:39 -04:00
• e8823a3709 r1027: renamed hifi to map-hifi; changed default Heng Li 2021-05-01 15:22:51 -04:00
• 7edeec67b0 r1026: fixed bugs in seed sampling add hifi Heng Li 2021-05-01 15:07:56 -04:00
• feb92d32ea r1025: seed rescuring Heng Li 2021-04-30 17:33:16 -04:00
• cdbd96be0c a bit refactoring for future changes Heng Li 2021-04-30 11:24:53 -04:00
• ba52c79024 added code of conduct Heng Li 2021-04-22 17:30:30 -04:00
• cd9ccfa069 r1022: check INDEL lengths in simple cases Heng Li 2021-04-11 22:07:00 -04:00
• 86b716448c larger window size for longer INDELs Heng Li 2021-04-11 16:08:29 -04:00
• 9ab95be1bb update END when it is not there Heng Li 2021-04-11 12:59:21 -04:00
• b51e859945 make sure ins/del match Heng Li 2021-04-11 11:47:14 -04:00
• a9037dc16c r1018: scripts for SV evaluation Heng Li 2021-04-11 01:08:17 -04:00
• 870f2cc2b9 updated the manpage Heng Li 2021-04-09 13:53:14 -04:00
• 9729fa99ad removed mappy.c Heng Li 2021-04-09 13:48:16 -04:00
• b6ff332de1 Release minimap2-2.18 (r1015) v2.18 Heng Li 2021-04-09 13:33:34 -04:00
• 77abafaaf3 prepare for release Heng Li 2021-04-09 13:18:56 -04:00
• 507d39af15 r1013: changed to a more accurate similarity est Heng Li 2021-04-08 13:57:53 -04:00
• 827ca4b461 r1012: fixed an off-by-one bug; resolves #489 Heng Li 2021-04-07 23:31:31 -04:00
• d3dde2fdd4 Convert from spaces to tabs. Marcus Stoiber 2021-04-05 08:54:08 -07:00
• 7db2e8d21a Convert python install from build_ext to setuptools setup_requires. Marcus Stoiber 2021-04-02 06:31:27 -07:00
• 0b41dd26a2 r1009: fixed a compiler warning Heng Li 2021-04-05 11:43:13 -04:00
• 2b47846cd6 r1008: don't parse space in BED Heng Li 2021-04-05 11:41:00 -04:00
• 67dd906a80 bump travis python version to 3.9 Heng Li 2021-03-23 09:12:49 -04:00
• 1b0bb7b0ba require overlap ratio when considering centromere Heng Li 2021-03-11 19:11:44 -05:00
• 1c4b7e8a48 explained --junc-bed in README Heng Li 2021-03-06 19:44:24 -05:00
• ecbc399fa2 improved sveval Heng Li 2021-03-06 19:44:13 -05:00
• 4dfd495cc2 added sveval Heng Li 2021-02-15 14:49:36 -05:00
• 194b457e79 option to print errors only Heng Li 2021-02-07 12:58:03 -05:00
• 75c8933511 evaluate large-scale misjoins Heng Li 2021-02-07 12:34:13 -05:00
• 1025993469 print number of errors on each read Heng Li 2021-01-29 14:08:21 -05:00
• a3253d1a6b added a command for simple VCF statistics Heng Li 2021-01-14 12:24:38 -05:00
• 2da649d1d7 Merge remote-tracking branch 'origin/master' Heng Li 2020-11-15 18:47:15 -05:00
• f995f55610 added --mask-len for #659 Heng Li 2020-08-21 11:12:50 -04:00
• c9874e2dc5 Initialize r->p if ez->zdropped Armin Töpfer 2020-06-12 12:52:08 +02:00
• 28a37a017a added utg error correction Heng Li 2020-05-01 00:45:05 -04:00
• ccb0f7b05d added a new Makefile for simde Heng Li 2020-04-25 22:43:29 -04:00
• 66db9da7d8 changed preprocessor conditionals for SIMDe mbrcic 2020-04-22 19:50:59 +02:00
• cd2b19035b r987: position on for strand wrongly outputted Heng Li 2020-04-22 10:31:25 -04:00
• 9c0e2c67f8 r986: don't estimate dv with --qstrand Heng Li 2020-04-21 13:21:03 -04:00
• da7109fd29 r985: optionally report cs/cg on the query strand Heng Li 2020-04-21 12:37:35 -04:00
• 2b3403f094 fix for Neon after test. mbrcic 2020-04-21 02:08:21 +02:00
• 3e16e4e39d Added documentation entry for added functionality, simde and no_simd. mbrcic 2020-04-21 01:36:19 +02:00
• f47e8a525e SIMDe made optional. Include paths changes for SIMDe. mbrcic 2020-04-21 01:08:32 +02:00
• c172df7d2d fix for Neon mbrcic 2020-04-20 21:14:15 +02:00
• 9e6fdd376b Changed sse2neon with SIMDe. Added building non-SIMD version. mbrcic 2020-04-20 18:28:06 +02:00
• 29f67a1666 r982: more accurate sum; output errors Heng Li 2020-04-14 16:18:53 -04:00
• adde608a42 Merge remote-tracking branch 'refs/remotes/origin/master' Heng Li 2020-04-14 15:52:57 -04:00
• f10dff78dc r981: asmgene to check duplicate genes Heng Li 2020-04-14 15:52:36 -04:00
• d97bba9f27 travis: added arm64 test. Jun Aruga 2020-04-13 11:35:20 +02:00
• 50775362bb r980: support auNGA Heng Li 2020-04-10 21:36:59 -04:00
• 0a5e386359 r979: fixed asmgene wrong report. Resolves #581. Heng Li 2020-04-06 19:57:15 -04:00
• cb56fb762a Merge branch 'master' of github.com:lh3/minimap2 Heng Li 2020-03-22 19:17:01 -04:00
• e2451e497a r975: asmstat without CIGAR/NM Heng Li 2020-03-22 19:16:43 -04:00
• d2de282d21 remove second definition of kstring Jared Simpson 2020-03-02 12:44:08 -05:00
• 48cb80ea94 change kstring_t integer storage size Jared Simpson 2020-02-19 09:35:49 -05:00
• 6a4b9f9082 r974: more informative msg on wrong FASTQ records Heng Li 2020-01-21 10:56:59 -05:00
• a7a01fe5bd r973: fixed compiling errors caused Heng Li 2020-01-21 10:43:31 -05:00
• 9dceae59a0 r972: renamed --alt-diff to --alt-drop Heng Li 2020-01-21 10:33:39 -05:00
• 20a3987082 Merge branch 'master' into alt Heng Li 2020-01-21 09:16:45 -05:00
• eb3ed6993d support ALT mapping Heng Li 2020-01-20 19:32:31 -05:00
• 7996f04008 r972: fixed negative de:f caused by ambiguous base Heng Li 2020-01-21 09:14:37 -05:00
• d2e14705e7 r968: allow large mini_batch; resolves #491 Heng Li 2020-01-18 12:24:44 -05:00
• 24f50f38e8 r967: no duplicated @SQ lines with --split-prefix Heng Li 2020-01-18 12:01:28 -05:00
• 04e015d803 r966: minimap2 returns 1 on file failure (#532) Heng Li 2020-01-18 10:58:59 -05:00
• 040f74102c r965: added --chain-gap-scale for #540 Heng Li 2020-01-18 10:29:33 -05:00
• dd3d637c20 Merge branch 'master' into avx avx Heng Li 2020-01-10 15:23:52 -05:00
• cdb7857841 r963: --junc-bonus not working; resolves #513 Heng Li 2020-01-06 22:03:50 -05:00
• 3c0d05d272 r962: abort given wrong RG line; resolves #541 Heng Li 2020-01-06 21:53:21 -05:00
• 47b646acbf r961: print indexed length Heng Li 2020-01-06 21:13:33 -05:00
• de6ad4c1d9 added two more filters occ-cutoff Heng Li 2019-12-24 00:06:44 -05:00
• 43b0399991 added --idx-min-occ and --idx-max-occ Heng Li 2019-12-23 22:58:44 -05:00
• a79cb3e991 Merge remote-tracking branch 'origin/master' Heng Li 2019-12-23 17:33:56 -05:00
• 367aed4271 added the asan and tsan targets to Makefile Heng Li 2019-12-23 17:33:10 -05:00
• 081df6ac7d Fix example.c seq read logic xdudiagnoa 2019-09-16 17:21:40 +08:00
• a3e7a575fb Add splice:hq to --help Torsten Seemann 2019-11-04 07:38:10 +11:00
• d90583b83c r954: fixed two potential undef behaviors (#443) Heng Li 2019-07-18 09:17:08 -04:00
• 7fc03b0c32 r953: krealloc is buggy Heng Li 2019-07-18 09:13:30 -04:00
• 20c104ce8d Report errno on file opening failures and I/O errors John Marshall 2019-07-17 11:43:54 +01:00
• 238b6bb3ea Fix memory leak in mappy.aligner.map. Marcus Stoiber 2019-07-05 12:23:53 -07:00
• e026e18439 added the description of "SA" tag. Closes #438 Heng Li 2019-07-01 09:18:33 -04:00
• 58c2251b18 compatibility with GenBank GTP (resolves $422) Heng Li 2019-06-11 09:16:03 -04:00
• 03dc8d5d97 test if index is built for #413 Heng Li 2019-06-07 09:11:11 -04:00
• 5cb61f8ee6 added FAQ Heng Li 2019-06-06 10:47:33 -04:00
• c18cd3ad2d Merge branch 'master' into avx Heng Li 2019-05-24 23:52:56 -04:00
• c16a1742a3 Er... Tavis doesn't have python 3.7. Heng Li 2019-05-11 20:06:48 -04:00
• 4bd5a018c2 test python 3.7 instead of 3.6 Heng Li 2019-05-11 20:05:06 -04:00
• 05974c80f1 r943: allow long ref name for --split-index Heng Li 2019-05-10 15:39:41 -04:00
• ee9f561e2f Update the manpage to v2.17 Heng Li 2019-05-05 09:30:56 -04:00
• 7bc87b4175 Release minimap2-2.17 (r941) v2.17 Heng Li 2019-05-04 23:49:17 -04:00
• 6762368cf0 r940: added the splice:hq preset Heng Li 2019-05-04 14:00:31 -04:00
• e60d78e0b1 Merge branch 'master' into avx Heng Li 2019-05-01 10:55:18 -04:00