aefa2c0d86
added --chain-skip-scale
2021-10-01 16:58:03 -04:00
05a8a45d44
r1105: avoid long running time occasionally ( #771 )
...
Caused by highly repetitive minimizers on a query sequence. The solution is to
filter out these query minimizers.
2021-08-15 19:43:01 -04:00
7358a1ead1
Release minimap2-2.22 (r1101)
2021-08-07 11:30:31 -04:00
32f552957e
Merge remote-tracking branch 'remotes/origin/master'
2021-08-07 10:40:02 -04:00
8a1d52bcbe
r1094: for --split-prefix update max_dp at the end
2021-08-06 21:40:43 -04:00
5180b70ff3
r1090: log wall-clock time for each read
2021-08-04 17:45:09 -04:00
2392e54fe2
r1089: fixed an unusual memory leak ( #749 )
...
This is more apparent when there are many candidate chains. Although only a
small numbers of them are extended, they are still occupying memory. A
realloc() solves this problem. This is a long existiing issue.
2021-08-04 17:07:00 -04:00
59488f0271
call mm_idx_destroy at the end of loop to fix memory leak
2021-07-26 18:25:08 -04:00
7e33fde82b
dev-r1087: added --cap-kalloc
2021-07-19 21:20:04 -04:00
83a535f148
dev-r1084: fixed flag integer overflow
2021-07-19 11:52:18 -04:00
1a8373bb84
dev-r1080: fixed negative dp_max
2021-07-18 21:07:14 -04:00
161ae7ff73
dev-r1079: per-read error rate
...
more tuning needed
2021-07-18 20:38:53 -04:00
8a6edab847
dev-r1078: decoupling ranking penalty
2021-07-18 16:22:48 -04:00
2546999639
dev-r1076: log gap penalty
2021-07-17 18:23:59 -04:00
5f449c5cae
fixed potential integer overflows
2021-07-16 17:20:05 -04:00
b046052d82
Merge branch 'master' into utec
2021-07-16 13:32:47 -04:00
581f2d7123
Release minimap2-2.21 (r1071)
2021-07-06 13:18:55 -04:00
52dbd439bc
r1080: re-versioning
2021-07-02 20:26:13 -04:00
459ce04c84
r1069: fixed a regression in comparison to v2.18
...
for PE short reads. An interesting omission. Resolves #776
2021-07-02 11:45:21 -04:00
e6cce019e4
r1068: fixed a bug caused by 3f71478
...
Resolves #752 (again)
2021-06-30 19:20:06 -04:00
fe6a0bb337
r1064: fixed another uninitialized condition
...
This one should also be harmless. It affects a min value, but that value is not
actually used.
2021-06-16 10:16:36 -04:00
3f7147864b
r1063: fixed an uninitialized access ( #752 )
...
This one is harmless.
2021-06-16 09:27:30 -04:00
15471bd629
Release minimap2-2.20 (r1061)
2021-05-27 15:26:04 -04:00
ca19463268
r1060: safer ways to use -rNUM1,NUM2
2021-05-27 10:55:13 -04:00
4f8d1bc360
r1059: with --rmq, use the larger bandwidth
2021-05-26 23:01:49 -04:00
9febf532c1
Release minimap2-2.19 (r1057)
2021-05-26 21:23:42 -04:00
ef09ccf104
Release minimap2-2.19 (r1055)
2021-05-26 21:01:03 -04:00
e74dfd1aa9
r1054: fixed a memory leak
2021-05-26 12:32:04 -04:00
41d7ccb191
r1052: default -g to 5k
2021-05-24 16:46:16 -04:00
34a41197d7
r1051: added two internal parameters
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rmq_rescue_size and rmq_rescue_ratio
2021-05-24 16:38:45 -04:00
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
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
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
b6ff332de1
Release minimap2-2.18 (r1015)
2021-04-09 13:33:34 -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
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
f995f55610
added --mask-len for #659
2020-08-21 11:12:50 -04:00
cd2b19035b
r987: position on for strand wrongly outputted
2020-04-22 10:31:25 -04:00
9c0e2c67f8
r986: don't estimate dv with --qstrand
2020-04-21 13:21:03 -04:00
Heng Li
Ryan Lim