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
...
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
6a4b9f9082
r974: more informative msg on wrong FASTQ records
...
Resolves #510
2020-01-21 10:56:59 -05:00
a7a01fe5bd
r973: fixed compiling errors caused
2020-01-21 10:43:31 -05:00
9dceae59a0
r972: renamed --alt-diff to --alt-drop
2020-01-21 10:33:39 -05:00
20a3987082
Merge branch 'master' into alt
2020-01-21 09:17:50 -05:00
eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -05:00
7996f04008
r972: fixed negative de:f caused by ambiguous base
2020-01-21 09:14:37 -05:00
d2e14705e7
r968: allow large mini_batch; resolves #491
2020-01-18 12:24:44 -05:00
24f50f38e8
r967: no duplicated @SQ lines with --split-prefix
...
resolves #527 and #400
2020-01-18 12:01:28 -05:00
04e015d803
r966: minimap2 returns 1 on file failure ( #532 )
2020-01-18 10:58:59 -05:00
040f74102c
r965: added --chain-gap-scale for #540
2020-01-18 10:29:33 -05:00
cdb7857841
r963: --junc-bonus not working; resolves #513
2020-01-06 22:03:50 -05:00
3c0d05d272
r962: abort given wrong RG line; resolves #541
2020-01-06 21:53:21 -05:00
47b646acbf
r961: print indexed length
2020-01-06 21:13:33 -05:00
a3e7a575fb
Add splice:hq to --help
2019-11-11 00:45:13 -05:00
d90583b83c
r954: fixed two potential undef behaviors ( #443 )
2019-07-18 09:17:08 -04:00
7fc03b0c32
r953: krealloc is buggy
...
Its use in minimap2 didn't trigger the bug, so the older minimap2 is still ok.
2019-07-18 09:13:30 -04:00
20c104ce8d
Report errno on file opening failures and I/O errors
...
Add the underlying operating system error (usually "No such file" or
"Out of space" respectively, but highly informative when it is not)
to these error messages.
2019-07-17 09:04:02 -04:00
05974c80f1
r943: allow long ref name for --split-index
...
Resolved #394 .
2019-05-10 15:39:41 -04:00
7bc87b4175
Release minimap2-2.17 (r941)
2019-05-04 23:49:17 -04:00
6762368cf0
r940: added the splice:hq preset
...
for high-quality CCS/mRNA splice alignment
2019-05-04 14:00:31 -04:00
c2aec88b84
r938: added --sam-hit-only; resolved #377
2019-04-30 22:40:36 -04:00
97f67a2a0a
r937: enlarge mm_mapopt_t::flag to 64 bits
2019-04-30 22:30:32 -04:00
69af86657e
r935: fixed a cigar like 5I6D7I; resolved #392
2019-04-30 21:35:24 -04:00
49c6d83a8e
r934: --junc-bed to read BED12
2019-04-28 20:12:28 -04:00
f64e426a5a
r933: resume versioning
2019-04-28 17:05:37 -04:00
f4c844b143
fixed a few simple bugs and leaks
2019-04-28 16:47:12 -04:00
Heng Li
Torsten Seemann
John Marshall