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
629c11728e
output the number of mismatches
2021-08-04 17:05:06 -04:00
7e33fde82b
dev-r1087: added --cap-kalloc
2021-07-19 21:20:04 -04:00
c4fe52fb07
reduced the default -l and -b
2021-07-19 17:25:11 -04:00
ead1cfbaca
output for binning
2021-07-19 14:56:33 -04:00
83a535f148
dev-r1084: fixed flag integer overflow
2021-07-19 11:52:18 -04:00
f3af29a8aa
don't add a new command
2021-07-19 10:57:48 -04:00
cf7eaef367
refactor and prepare for a new command
2021-07-19 00:36:17 -04:00
2411887d8e
rename
2021-07-19 00:30:16 -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
15118dd521
output #mismatches/#dels/#ins in view
2021-07-18 15:13:40 -04:00
2546999639
dev-r1076: log gap penalty
2021-07-17 18:23:59 -04:00
52fafe0fed
updated pbsim to pbsim2
2021-07-17 18:18:26 -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
260a68d232
Use #defines for CIGAR operators in C code
...
Give the CIGAR constants names to clarify the code. So that ksw2.h
remains self-contained, define KSW_* versions of the CIGAR operators
it needs for use within ksw2.h. Other code should in general use the
full set of MM_CIGAR_* constants in minimap.h.
2021-07-02 13:03:03 -04:00
177eef259d
Use the full MIDNSHP=X string whenever printing CIGAR strings
...
Define MM_CIGAR_STR to the full string of CIGAR operators (including
the 'B' operator as well) and use it throughout the C code.
It would be possible to use it from the Cython code too, but it's easier
to keep that as a Cython string literal to avoid adding extra runtime
code to handle locale conversion.
2021-07-02 13:03:03 -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
7025b0b941
Merge branch 'master' of github.com:lh3/minimap2
2021-06-16 10:18:40 -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
c83589b9ea
Update README.md
...
Clarification on approximate mapping
2021-06-10 09:36:39 -04:00
ce7a59f412
Fixed a typo in README
...
I just hate my butterfly keyboard!
2021-05-27 15:43:04 -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
1776c0c645
missing seed.c in setup.py
...
Ok, I am not going to re-release again...
2021-05-26 21:36:09 -04:00
9febf532c1
Release minimap2-2.19 (r1057)
2021-05-26 21:23:42 -04:00
cec23131e4
fixed a python compilation error
...
Caused by chain.c -> lchain.c
2021-05-26 21:20:48 -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
f31705bb4a
r1053: made junceval work with PAF
2021-05-26 11:54:46 -04:00
41d7ccb191
r1052: default -g to 5k
2021-05-24 16:46:16 -04:00
34a41197d7
r1051: added two internal parameters
...
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
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
Heng Li
John Marshall
Torsten Houwaart
Ariel Erijman