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379728726a084d0921a5f6396df36ae530e66ac5
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972 Commits

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Author SHA1 Message Date
Heng Li
379728726a r1049: removed the long-join heuristics 2021-05-24 16:21:40 -04:00
Heng Li
4f91558160 r1048: rescue long gaps 2021-05-24 16:09:09 -04:00
Heng Li
ec3bc6efd7 r1047: make gap penalty proportional to k-mer 
closer to the older minimap2
 2021-05-24 13:18:17 -04:00
Heng Li
8ec8866100 Merge branch 'master' into dev-rmq 2021-05-23 21:01:04 -04:00
Heng Li
9e7247cff9 sync python with recent changes 2021-05-23 21:00:15 -04:00
Ariel Erijman
cd66777bfb small typo 2021-05-23 13:09:55 -04:00
Heng Li
5d7d25e92d Merge remote-tracking branch 'origin/master' 2021-05-23 13:08:52 -04:00
Heng Li
2a3793bbd2 clarify that map-hifi is for HEAD only 
Resolves #747
 2021-05-23 13:08:15 -04:00
Heng Li
f97008a10e Merge branch 'master' into dev-rmq 2021-05-20 19:36:33 -04:00
Cornelius Roemer
10502e2a78 Fixed typo in Readme.md 
deltion -> deletion
 2021-05-14 15:38:30 -04:00
Don Kirkby
4422c0c6f9 Typo fix in Python README. 
Thanks for sharing minimap2. Here's a little fix.
 2021-05-14 15:38:12 -04:00
Heng Li
42a11e1d58 Changed Travis to Github Actions in README 2021-05-10 12:58:25 -04:00
Heng Li
76df351fa8 added github action 2021-05-10 12:55:58 -04:00
Heng Li
d065d3bead Merge branch 'master' into dev-rmq 2021-05-10 12:42:57 -04:00
Heng Li
ac146fe7bc r1035: failed to index under the --frag=yes mode 
Resolves #734
 2021-05-10 12:36:48 -04:00
Heng Li
6c96078ed0 r1034: changed multiple defaults; updated manpage 2021-05-03 22:51:34 -04:00
Heng Li
bbb4f97e52 support RMQ 2021-05-03 09:27:04 -04:00
Heng Li
b7f4d8a0f4 removed the old minimap2 chaining 2021-05-02 18:55:37 -04:00
Heng Li
e81927e7a1 prepare to backport unimap/minigraph chaining 2021-05-02 18:25:49 -04:00
Heng Li
f7dc5799c5 clarify CLR when necessary 2021-05-01 15:56:33 -04:00
Heng Li
817cb81cb0 Updated README for the HiFi preset 2021-05-01 15:47:25 -04:00
Heng Li
0f5608c4a4 r1028: backport minigraph -U 2021-05-01 15:41:39 -04:00
Heng Li
e8823a3709 r1027: renamed hifi to map-hifi; changed default 2021-05-01 15:22:51 -04:00
Heng Li
7edeec67b0 r1026: fixed bugs in seed sampling add hifi 2021-05-01 15:07:56 -04:00
Heng Li
feb92d32ea r1025: seed rescuring 2021-04-30 17:33:16 -04:00
Heng Li
cdbd96be0c a bit refactoring for future changes 2021-04-30 11:24:53 -04:00
Heng Li
ba52c79024 added code of conduct 2021-04-22 17:30:30 -04:00
Heng Li
cd9ccfa069 r1022: check INDEL lengths in simple cases 2021-04-11 22:07:00 -04:00
Heng Li
86b716448c larger window size for longer INDELs 2021-04-11 16:08:29 -04:00
Heng Li
9ab95be1bb update END when it is not there 2021-04-11 12:59:21 -04:00
Heng Li
b51e859945 make sure ins/del match 2021-04-11 11:47:14 -04:00
Heng Li
a9037dc16c r1018: scripts for SV evaluation 2021-04-11 01:08:17 -04:00
Heng Li
9729fa99ad removed mappy.c 2021-04-09 13:48:16 -04:00
Heng Li
b6ff332de1 Release minimap2-2.18 (r1015) v2.18 2021-04-09 13:33:34 -04:00
Heng Li
77abafaaf3 prepare for release 2021-04-09 13:18:56 -04:00
Heng Li
507d39af15 r1013: changed to a more accurate similarity est 
Based on DOI:10.1101/2021.01.15.426881. One minimap2 reviewer suggested the
right formula to me but I thought the difference would be insignificant. I was
wrong.
 2021-04-08 13:57:53 -04:00
Heng Li
827ca4b461 r1012: fixed an off-by-one bug; resolves #489 2021-04-07 23:31:31 -04:00
Marcus Stoiber
d3dde2fdd4 Convert from spaces to tabs. 2021-04-05 11:55:10 -04:00
Marcus Stoiber
7db2e8d21a Convert python install from build_ext to setuptools setup_requires. 2021-04-05 11:55:10 -04:00
Heng Li
0b41dd26a2 r1009: fixed a compiler warning 2021-04-05 11:43:13 -04:00
Heng Li
2b47846cd6 r1008: don't parse space in BED 2021-04-05 11:41:00 -04:00
Heng Li
67dd906a80 bump travis python version to 3.9 2021-03-23 09:12:49 -04:00
Heng Li
1b0bb7b0ba require overlap ratio when considering centromere 2021-03-11 19:11:44 -05:00
Heng Li
1c4b7e8a48 explained --junc-bed in README 2021-03-06 19:44:24 -05:00
Heng Li
ecbc399fa2 improved sveval 2021-03-06 19:44:13 -05:00
Heng Li
4dfd495cc2 added sveval 2021-02-15 14:49:36 -05:00
Heng Li
194b457e79 option to print errors only 2021-02-07 12:58:03 -05:00
Heng Li
75c8933511 evaluate large-scale misjoins 2021-02-07 12:34:13 -05:00
Heng Li
1025993469 print number of errors on each read 2021-01-29 14:08:21 -05:00
Heng Li
a3253d1a6b added a command for simple VCF statistics 2021-01-14 12:24:38 -05:00