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
6420acca6d
BED I/O
2019-04-28 16:47:12 -04:00
6b391e3373
Release minimap2-2.16 (r922)
2019-02-28 15:49:24 -05:00
55e39c2d30
r921: output unmapped reads in full PAF
2019-02-27 15:03:19 -05:00
90b7b83ec7
fix typo in command line help
2019-02-27 14:46:57 -05:00
d431dc0181
r917: added --max-chain-iter to avoid worst case
...
Resolves #324
2019-02-27 14:41:01 -05:00
ea84fc0a53
r917: fixed a bug in command-line parsing
...
Resolves #344
2019-02-27 11:22:58 -05:00
e02bebd96d
r915: fixed a bug caused by the latest change
2019-02-14 10:04:04 -05:00
32ab6ce15b
r914: fixed two harmless division by 0
...
Resolves #326
2019-02-12 19:30:49 -05:00
1739a260fb
r913: output tag "rl", length of unseedable regs
2019-02-05 14:19:17 -05:00
8b05880f73
r911: option -o to output to file ( #319 )
2019-01-29 10:42:20 -05:00
eba237f39d
r910: meaningful error message ( #320 )
...
when minimap2 fails to create temporary files
2019-01-29 10:29:27 -05:00
597212b9f3
r908: added an assertion to detect a potential bug
...
as in #311
2019-01-23 11:18:50 -05:00
48e230f40d
r906: de tag is wrongly calculated given "N"
...
Resolves #309
2019-01-11 19:39:09 -05:00
c404f49569
Release minimap2-2.15 (r905)
2019-01-10 12:34:45 -05:00
cf2bae6e9b
r904: fixed a corner-case segfault. Resolves #307 .
2019-01-10 09:57:05 -05:00
ea2b1c5b2a
r894: added --max-qlen to filter out long query
2018-12-12 12:27:32 -05:00
2c52364527
r892: avoid de:f:0.0000
2018-11-24 21:54:28 -05:00
128476efc9
r891: compute gap-compressed divergence
2018-11-24 21:50:49 -05:00
1b3a6a0fe5
r890: removed "register" ( #261 )
2018-11-19 13:57:31 -05:00
83a8ee7038
r888: fixed incorrect CIGAR when --eqx in use
...
This was caused by mm_fix_cigar() which may change query/target offset in very
rare cases. Generating EQX has to beware of this change.
Resolves #266
2018-11-18 14:22:29 -05:00
91f548b497
r886: fixed two minor typos
...
Resolves #264
Resolves #265
2018-11-08 12:04:14 -05:00
6596c63dcd
r884: for C++ compatibility ( #261 )
2018-11-06 22:07:11 -05:00
59f23f7579
Release minimap2-2.14 (r883)
2018-11-06 00:03:16 -05:00
5e55e397e9
r882: guard against -E0 ( #263 )
2018-11-05 23:36:12 -05:00
Heng Li
Torsten Seemann
John Marshall
Kevin Chan