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
da7109fd29
r985: optionally report cs/cg on the query strand
...
PAF only; not well tested
2020-04-21 12:37:35 -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
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
88c421e8de
r881: a recent change reduces sr accuracy
2018-11-05 22:03:59 -05:00
3db5bfe6e5
r880: fixed false wrong FASTA/Q alert
2018-11-05 20:52:07 -05:00
1ede8ca170
r877: renamed cap-sw-mat to cap-sw-mem
2018-11-05 11:46:38 -05:00
13981404e2
r876: skip DP if taking too much RAM ( #259 )
2018-11-05 11:43:10 -05:00
fd64dd26f6
r875: warn given incorrect FASTA/Q
...
resolves #252
resolves #255
2018-11-05 10:02:44 -05:00
24df95e4b8
r874: don't call x86_simd() so often
...
This takes a few percent of time in profiler.
2018-11-05 09:20:35 -05:00
a8ee48c2ce
r873: comforming to C99/C11; resolves #261
2018-11-05 08:25:07 -05:00
42baf287a4
r866: fixed a typo; resolves #262
2018-10-30 09:11:55 -04:00
9ed56b4a25
r860: MD/cs not working with --eqx
2018-10-26 23:23:53 -04:00
377c7099a8
r858: fixed a bug; resolves #254
2018-10-22 22:47:11 -04:00
7b0a49732e
r856: wrongly reported for an unrecognized option
...
Resolved #250
2018-10-19 20:07:14 -04:00
d04ac068fd
r852: a minor when large --end-bonus is in use
...
We may use a large --end-bonus to mimic end-to-end alignment. In the short-read
mode, the candidate alignment region may be out of the band, which leads to
truncated alignment.
2018-10-15 21:28:27 -04:00
5d5d392c02
Release minimap2-2.13 (r850)
2018-10-11 13:18:31 -04:00
170863e553
r849: option -P doesn't work
...
I don't know why I haven't found it at the beginning.
2018-10-04 16:11:59 -04:00
97f97306a4
r847: guard against -N0
2018-09-27 15:13:44 -04:00
1077b7ddc8
r846: added --hard-mask-level for #244
2018-09-27 14:46:26 -04:00
c57b59f02f
r845: log peak memory
2018-09-23 20:27:49 -04:00
c63a33904f
r836: fixed an integer overflow
...
Forgot this one.
2018-09-14 23:29:31 -04:00
70b0fede64
r835: improved help message. Resolved #232
2018-09-14 22:29:25 -04:00
7d80d6de4a
r832: fixed outdated -L. Resolved #231 and #233
2018-09-14 22:21:33 -04:00
7998fe9906
r829: replaced musl's getopt with ketopt
2018-09-01 21:18:02 -04:00
3a119d606f
r828: --MD to support spliced alignment
2018-08-22 10:47:45 -04:00
a5eafb75f9
Release minimap2-2.12 (r827)
2018-08-06 12:44:39 -04:00
b0f39a1a61
r823: mappy to index a single sequence
2018-08-05 20:57:05 -04:00
5ab6538757
r822: added option --no-end-flt
2018-08-05 19:42:12 -04:00
b32296e18f
r821: fixed memory when -y is used
2018-07-31 15:14:37 -04:00
ff9917a1c4
r819: mappy to support cs/MD
2018-07-24 23:29:55 -04:00
395c8d678a
r815: fixed a memory leak
2018-07-15 22:11:32 -04:00
830da7fa27
r814: resumed versioning
2018-07-15 11:48:14 -04:00
a655cbef86
print SAM header; remove tmp files
2018-07-15 11:03:18 -04:00
e5277dbf5c
code backup
2018-07-14 22:52:36 -04:00
1a55227d5a
write hits to tmp files (unfinished)
2018-07-14 12:15:10 -04:00
a609a07f8c
optionally output unmapped query in PAF
2018-07-07 10:26:08 -05:00
0517972d02
Release minimap2-2.11 (r797)
2018-06-21 00:04:08 -04:00
d46e68e6ad
r796: don't use ssize_t
2018-06-20 12:45:27 -04:00
2584a4149a
r295: use -r2000 for ava-ont, NOT for ava-pb
2018-06-20 12:24:43 -04:00
Heng Li
Torsten Seemann
John Marshall
Kevin Chan