9626b3e716
r1050: -r accepts two bandwidths
2021-05-24 16:29:21 -04:00
379728726a
r1049: removed the long-join heuristics
2021-05-24 16:21:40 -04:00
4f91558160
r1048: rescue long gaps
2021-05-24 16:09:09 -04:00
ec3bc6efd7
r1047: make gap penalty proportional to k-mer
...
closer to the older minimap2
2021-05-24 13:18:17 -04:00
8ec8866100
Merge branch 'master' into dev-rmq
2021-05-23 21:01:04 -04:00
9e7247cff9
sync python with recent changes
2021-05-23 21:00:15 -04:00
cd66777bfb
small typo
2021-05-23 13:09:55 -04:00
5d7d25e92d
Merge remote-tracking branch 'origin/master'
2021-05-23 13:08:52 -04:00
2a3793bbd2
clarify that map-hifi is for HEAD only
...
Resolves #747
2021-05-23 13:08:15 -04:00
f97008a10e
Merge branch 'master' into dev-rmq
2021-05-20 19:36:33 -04:00
10502e2a78
Fixed typo in Readme.md
...
deltion -> deletion
2021-05-14 15:38:30 -04:00
4422c0c6f9
Typo fix in Python README.
...
Thanks for sharing minimap2. Here's a little fix.
2021-05-14 15:38:12 -04:00
42a11e1d58
Changed Travis to Github Actions in README
2021-05-10 12:58:25 -04:00
76df351fa8
added github action
2021-05-10 12:55:58 -04:00
d065d3bead
Merge branch 'master' into dev-rmq
2021-05-10 12:42:57 -04:00
ac146fe7bc
r1035: failed to index under the --frag=yes mode
...
Resolves #734
2021-05-10 12:36:48 -04:00
6c96078ed0
r1034: changed multiple defaults; updated manpage
2021-05-03 22:51:34 -04:00
bbb4f97e52
support RMQ
2021-05-03 09:27:04 -04:00
b7f4d8a0f4
removed the old minimap2 chaining
2021-05-02 18:55:37 -04:00
e81927e7a1
prepare to backport unimap/minigraph chaining
2021-05-02 18:25:49 -04:00
f7dc5799c5
clarify CLR when necessary
2021-05-01 15:56:33 -04:00
817cb81cb0
Updated README for the HiFi preset
2021-05-01 15:47:25 -04:00
0f5608c4a4
r1028: backport minigraph -U
2021-05-01 15:41:39 -04:00
e8823a3709
r1027: renamed hifi to map-hifi; changed default
2021-05-01 15:22:51 -04:00
7edeec67b0
r1026: fixed bugs in seed sampling add hifi
2021-05-01 15:07:56 -04:00
feb92d32ea
r1025: seed rescuring
2021-04-30 17:33:16 -04:00
cdbd96be0c
a bit refactoring for future changes
2021-04-30 11:24:53 -04:00
ba52c79024
added code of conduct
2021-04-22 17:30:30 -04:00
cd9ccfa069
r1022: check INDEL lengths in simple cases
2021-04-11 22:07:00 -04:00
86b716448c
larger window size for longer INDELs
2021-04-11 16:08:29 -04:00
9ab95be1bb
update END when it is not there
2021-04-11 12:59:21 -04:00
b51e859945
make sure ins/del match
2021-04-11 11:47:14 -04:00
a9037dc16c
r1018: scripts for SV evaluation
2021-04-11 01:08:17 -04:00
9729fa99ad
removed mappy.c
2021-04-09 13:48:16 -04:00
b6ff332de1
Release minimap2-2.18 (r1015)
2021-04-09 13:33:34 -04:00
77abafaaf3
prepare for release
2021-04-09 13:18:56 -04:00
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
827ca4b461
r1012: fixed an off-by-one bug; resolves #489
2021-04-07 23:31:31 -04:00
d3dde2fdd4
Convert from spaces to tabs.
2021-04-05 11:55:10 -04:00
7db2e8d21a
Convert python install from build_ext to setuptools setup_requires.
2021-04-05 11:55:10 -04:00
0b41dd26a2
r1009: fixed a compiler warning
2021-04-05 11:43:13 -04:00
2b47846cd6
r1008: don't parse space in BED
2021-04-05 11:41:00 -04:00
67dd906a80
bump travis python version to 3.9
2021-03-23 09:12:49 -04:00
1b0bb7b0ba
require overlap ratio when considering centromere
2021-03-11 19:11:44 -05:00
1c4b7e8a48
explained --junc-bed in README
2021-03-06 19:44:24 -05:00
ecbc399fa2
improved sveval
2021-03-06 19:44:13 -05:00
4dfd495cc2
added sveval
2021-02-15 14:49:36 -05:00
194b457e79
option to print errors only
2021-02-07 12:58:03 -05:00
75c8933511
evaluate large-scale misjoins
2021-02-07 12:34:13 -05:00
1025993469
print number of errors on each read
2021-01-29 14:08:21 -05:00
Heng Li
Ariel Erijman
Cornelius Roemer
Don Kirkby
Marcus Stoiber