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  • 8a6edab847 dev-r1078: decoupling ranking penalty Heng Li 2021-07-18 16:22:48 -0400
  • 15118dd521 output #mismatches/#dels/#ins in view Heng Li 2021-07-18 15:13:40 -0400
  • 2546999639 dev-r1076: log gap penalty Heng Li 2021-07-17 18:23:59 -0400
  • 52fafe0fed updated pbsim to pbsim2 Heng Li 2021-07-17 18:18:26 -0400
  • 5f449c5cae fixed potential integer overflows Heng Li 2021-07-16 17:20:05 -0400
  • b046052d82 Merge branch 'master' into utec Heng Li 2021-07-16 13:32:47 -0400
  • 5cc3d2239f missing target object files from Makefile.simde to fix issue #779 Jason Stajich 2021-07-06 22:57:07 -0700
  • 581f2d7123 Release minimap2-2.21 (r1071) Heng Li 2021-07-06 13:18:55 -0400
  • 52dbd439bc r1080: re-versioning Heng Li 2021-07-02 20:26:13 -0400
  • 260a68d232 Use #defines for CIGAR operators in C code John Marshall 2021-04-10 12:49:39 +0100
  • 177eef259d Use the full MIDNSHP=X string whenever printing CIGAR strings John Marshall 2021-04-09 19:34:53 +0100
  • 459ce04c84 r1069: fixed a regression in comparison to v2.18 Heng Li 2021-07-02 11:45:21 -0400
  • e6cce019e4 r1068: fixed a bug caused by 3f71478 Heng Li 2021-06-30 19:20:06 -0400
  • 7025b0b941 Merge branch 'master' of github.com:lh3/minimap2 Heng Li 2021-06-16 10:18:40 -0400
  • fe6a0bb337 r1064: fixed another uninitialized condition Heng Li 2021-06-16 10:16:36 -0400
  • 3f7147864b r1063: fixed an uninitialized access (#752) Heng Li 2021-06-16 09:27:30 -0400
  • c83589b9ea Update README.md Torsten Houwaart 2021-06-07 15:31:58 +0200
  • ce7a59f412 Fixed a typo in README Heng Li 2021-05-27 15:43:04 -0400
  • 15471bd629 Release minimap2-2.20 (r1061) Heng Li 2021-05-27 15:26:04 -0400
  • ca19463268 r1060: safer ways to use -rNUM1,NUM2 Heng Li 2021-05-27 10:55:13 -0400
  • 4f8d1bc360 r1059: with --rmq, use the larger bandwidth Heng Li 2021-05-26 23:01:49 -0400
  • 1776c0c645 missing seed.c in setup.py Heng Li 2021-05-26 21:36:09 -0400
  • 9febf532c1 Release minimap2-2.19 (r1057) Heng Li 2021-05-26 21:23:42 -0400
  • cec23131e4 fixed a python compilation error Heng Li 2021-05-26 21:20:48 -0400
  • ef09ccf104 Release minimap2-2.19 (r1055) Heng Li 2021-05-26 21:01:03 -0400
  • e74dfd1aa9 r1054: fixed a memory leak Heng Li 2021-05-26 12:32:04 -0400
  • f31705bb4a r1053: made junceval work with PAF Heng Li 2021-05-26 11:54:46 -0400
  • 41d7ccb191 r1052: default -g to 5k Heng Li 2021-05-24 16:46:16 -0400
  • 34a41197d7 r1051: added two internal parameters Heng Li 2021-05-24 16:38:45 -0400
  • 9626b3e716 r1050: -r accepts two bandwidths Heng Li 2021-05-24 16:29:21 -0400
  • 379728726a r1049: removed the long-join heuristics Heng Li 2021-05-24 16:21:40 -0400
  • 4f91558160 r1048: rescue long gaps Heng Li 2021-05-24 16:09:09 -0400
  • ec3bc6efd7 r1047: make gap penalty proportional to k-mer Heng Li 2021-05-24 13:18:17 -0400
  • 8ec8866100 Merge branch 'master' into dev-rmq Heng Li 2021-05-23 21:01:04 -0400
  • 9e7247cff9 sync python with recent changes Heng Li 2021-05-23 21:00:15 -0400
  • cd66777bfb small typo Ariel Erijman 2021-05-19 13:58:14 -0400
  • 5d7d25e92d Merge remote-tracking branch 'origin/master' Heng Li 2021-05-23 13:08:52 -0400
  • 2a3793bbd2 clarify that map-hifi is for HEAD only Heng Li 2021-05-23 13:08:15 -0400
  • f97008a10e Merge branch 'master' into dev-rmq Heng Li 2021-05-20 19:36:33 -0400
  • 10502e2a78 Fixed typo in Readme.md Cornelius Roemer 2021-05-13 17:55:47 +0200
  • 4422c0c6f9 Typo fix in Python README. Don Kirkby 2021-05-14 12:16:12 -0700
  • 42a11e1d58 Changed Travis to Github Actions in README Heng Li 2021-05-10 12:58:25 -0400
  • 76df351fa8 added github action Heng Li 2021-05-10 12:55:58 -0400
  • d065d3bead Merge branch 'master' into dev-rmq Heng Li 2021-05-10 12:42:57 -0400
  • ac146fe7bc r1035: failed to index under the --frag=yes mode Heng Li 2021-05-10 12:36:48 -0400
  • 6c96078ed0 r1034: changed multiple defaults; updated manpage Heng Li 2021-05-03 22:51:34 -0400
  • bbb4f97e52 support RMQ Heng Li 2021-05-03 09:27:04 -0400
  • b7f4d8a0f4 removed the old minimap2 chaining Heng Li 2021-05-02 18:55:37 -0400
  • e81927e7a1 prepare to backport unimap/minigraph chaining Heng Li 2021-05-02 18:25:49 -0400
  • f7dc5799c5 clarify CLR when necessary Heng Li 2021-05-01 15:56:33 -0400
  • 817cb81cb0 Updated README for the HiFi preset Heng Li 2021-05-01 15:47:25 -0400
  • 0f5608c4a4 r1028: backport minigraph -U Heng Li 2021-05-01 15:41:39 -0400
  • e8823a3709 r1027: renamed hifi to map-hifi; changed default Heng Li 2021-05-01 15:22:51 -0400
  • 7edeec67b0 r1026: fixed bugs in seed sampling add hifi Heng Li 2021-05-01 15:07:56 -0400
  • feb92d32ea r1025: seed rescuring Heng Li 2021-04-30 17:33:16 -0400
  • cdbd96be0c a bit refactoring for future changes Heng Li 2021-04-30 11:24:53 -0400
  • ba52c79024 added code of conduct Heng Li 2021-04-22 17:30:30 -0400
  • cd9ccfa069 r1022: check INDEL lengths in simple cases Heng Li 2021-04-11 22:07:00 -0400
  • 86b716448c larger window size for longer INDELs Heng Li 2021-04-11 16:08:29 -0400
  • 9ab95be1bb update END when it is not there Heng Li 2021-04-11 12:59:21 -0400
  • b51e859945 make sure ins/del match Heng Li 2021-04-11 11:47:14 -0400
  • a9037dc16c r1018: scripts for SV evaluation Heng Li 2021-04-11 01:08:17 -0400
  • 9729fa99ad removed mappy.c Heng Li 2021-04-09 13:48:16 -0400
  • b6ff332de1 Release minimap2-2.18 (r1015) Heng Li 2021-04-09 13:33:34 -0400
  • 77abafaaf3 prepare for release Heng Li 2021-04-09 13:18:56 -0400
  • 507d39af15 r1013: changed to a more accurate similarity est Heng Li 2021-04-08 13:57:53 -0400
  • 827ca4b461 r1012: fixed an off-by-one bug; resolves #489 Heng Li 2021-04-07 23:31:31 -0400
  • d3dde2fdd4 Convert from spaces to tabs. Marcus Stoiber 2021-04-05 08:54:08 -0700
  • 7db2e8d21a Convert python install from build_ext to setuptools setup_requires. Marcus Stoiber 2021-04-02 06:31:27 -0700
  • 0b41dd26a2 r1009: fixed a compiler warning Heng Li 2021-04-05 11:43:13 -0400
  • 2b47846cd6 r1008: don't parse space in BED Heng Li 2021-04-05 11:41:00 -0400
  • 67dd906a80 bump travis python version to 3.9 Heng Li 2021-03-23 09:12:49 -0400
  • 1b0bb7b0ba require overlap ratio when considering centromere Heng Li 2021-03-11 19:11:44 -0500
  • 1c4b7e8a48 explained --junc-bed in README Heng Li 2021-03-06 19:44:24 -0500
  • ecbc399fa2 improved sveval Heng Li 2021-03-06 19:44:13 -0500
  • 4dfd495cc2 added sveval Heng Li 2021-02-15 14:49:36 -0500
  • 194b457e79 option to print errors only Heng Li 2021-02-07 12:58:03 -0500
  • 75c8933511 evaluate large-scale misjoins Heng Li 2021-02-07 12:34:13 -0500
  • 1025993469 print number of errors on each read Heng Li 2021-01-29 14:08:21 -0500
  • a3253d1a6b added a command for simple VCF statistics Heng Li 2021-01-14 12:24:38 -0500
  • 2da649d1d7 Merge remote-tracking branch 'origin/master' Heng Li 2020-11-15 18:47:15 -0500
  • f995f55610 added --mask-len for #659 Heng Li 2020-08-21 11:12:50 -0400
  • c9874e2dc5 Initialize r->p if ez->zdropped Armin Töpfer 2020-06-12 12:52:08 +0200
  • 28a37a017a added utg error correction Heng Li 2020-05-01 00:45:05 -0400
  • ccb0f7b05d added a new Makefile for simde Heng Li 2020-04-25 22:43:29 -0400
  • 66db9da7d8 changed preprocessor conditionals for SIMDe mbrcic 2020-04-22 19:50:59 +0200
  • cd2b19035b r987: position on for strand wrongly outputted Heng Li 2020-04-22 10:31:25 -0400
  • 9c0e2c67f8 r986: don't estimate dv with --qstrand Heng Li 2020-04-21 13:21:03 -0400
  • da7109fd29 r985: optionally report cs/cg on the query strand Heng Li 2020-04-21 12:37:35 -0400
  • 2b3403f094 fix for Neon after test. mbrcic 2020-04-21 02:08:21 +0200
  • 3e16e4e39d Added documentation entry for added functionality, simde and no_simd. mbrcic 2020-04-21 01:36:19 +0200
  • f47e8a525e SIMDe made optional. Include paths changes for SIMDe. mbrcic 2020-04-21 01:08:32 +0200
  • c172df7d2d fix for Neon mbrcic 2020-04-20 21:14:15 +0200
  • 9e6fdd376b Changed sse2neon with SIMDe. Added building non-SIMD version. mbrcic 2020-04-20 18:28:06 +0200
  • 29f67a1666 r982: more accurate sum; output errors Heng Li 2020-04-14 16:18:53 -0400
  • adde608a42 Merge remote-tracking branch 'refs/remotes/origin/master' Heng Li 2020-04-14 15:52:57 -0400
  • f10dff78dc r981: asmgene to check duplicate genes Heng Li 2020-04-14 15:52:36 -0400
  • d97bba9f27 travis: added arm64 test. Jun Aruga 2020-04-13 11:35:20 +0200
  • 50775362bb r980: support auNGA Heng Li 2020-04-10 21:36:59 -0400
  • 0a5e386359 r979: fixed asmgene wrong report. Resolves #581. Heng Li 2020-04-06 19:57:15 -0400