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
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
2bb8cbbeef
updated manpage
2019-04-28 17:02:49 -04:00
169216bfff
manpage was wrongly marked as "dirty"
2019-02-28 15:58:12 -05:00
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
d431dc0181
r917: added --max-chain-iter to avoid worst case
...
Resolves #324
2019-02-27 14:41:01 -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
c404f49569
Release minimap2-2.15 (r905)
2019-01-10 12:34:45 -05:00
ea2b1c5b2a
r894: added --max-qlen to filter out long query
2018-12-12 12:27:32 -05:00
128476efc9
r891: compute gap-compressed divergence
2018-11-24 21:50:49 -05:00
59f23f7579
Release minimap2-2.14 (r883)
2018-11-06 00:03:16 -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
2ceba22a7a
fixed a typo in manpage
2018-10-28 11:51:02 -04:00
ecb6c5c36c
Document --no-pairing ( #256 )
2018-10-23 10:00:21 -04:00
5d5d392c02
Release minimap2-2.13 (r850)
2018-10-11 13:18:31 -04:00
1077b7ddc8
r846: added --hard-mask-level for #244
2018-09-27 14:46:26 -04:00
a5eafb75f9
Release minimap2-2.12 (r827)
2018-08-06 12:44:39 -04:00
5ab6538757
r822: added option --no-end-flt
2018-08-05 19:42:12 -04:00
395c8d678a
r815: fixed a memory leak
2018-07-15 22:11:32 -04:00
0517972d02
Release minimap2-2.11 (r797)
2018-06-21 00:04:08 -04:00
154d2caf5b
r784: support the =/X CIGAR operators ( #156 )
2018-05-30 16:11:22 -04:00
734ac379bb
r770: matching N bases not working properly ( #155 )
2018-04-30 19:55:23 -04:00
aef7b0744c
r768: shortened preset; added dv tag ( #25 )
...
Also added asm20 to command line help (#151 )
2018-04-24 12:48:54 -04:00
2d7ec75d50
Release minimap2-2.10 (r761)
2018-03-27 11:45:44 -04:00
5ef9580b17
r753: change bandwidth in ava-ont to 2000bp
2018-03-23 10:15:23 -04:00
08bd2123b6
r752: option to copy comments to output ( #136 )
2018-03-23 10:04:33 -04:00
8766d286df
r751: optionally output MD ( #118 )
2018-03-22 14:15:33 -04:00
d135feb1a5
response to reviewers' comments, round 2
2018-03-15 21:59:57 -04:00
bdc615c1d4
r741: added --min-occ-floor to improve #107
2018-03-12 14:32:27 -04:00
eeb314edd6
Release minimap2-2.9 (r720)
2018-02-24 09:31:09 -05:00
54a42aafe5
keep documents in sync
2018-02-15 17:21:09 -05:00
997ab9bb2e
Fixed the description of --dual
2018-02-01 15:11:51 -05:00
53ce317e59
Release minimap2-2.8 (r672)
2018-02-01 12:50:20 -05:00
da6947cfa3
r671: cleanup command line options
2018-01-31 13:59:52 -05:00
6205fa6f21
document --heap-sort
2018-01-26 15:15:40 -05:00
0454e6be91
explain -M in the manpage
2018-01-18 11:47:11 -05:00
33f8157961
r655: options to map to one strand of the ref #91
2018-01-16 10:34:30 -05:00
eecc06086f
Released minimap2-2.7 (r654)
2018-01-09 13:16:00 -05:00
eb819c29e8
Release minimap2-2.6 (r623)
2017-12-12 11:09:59 -05:00
98a6e52c06
r618: heuristics to avoid tiny terminal exons
2017-12-11 00:57:55 -05:00
0e42628ef6
r611: document --idx-no-seq; better inv aln
2017-12-08 13:16:18 -05:00
3b518271ee
Release minimap2-2.5 (r572)
2017-11-11 11:29:28 -05:00
99a2709913
r567: minor change to #56
2017-11-09 19:17:45 -05:00
21a46ba652
Release minimap2-2.4 (r555)
2017-11-06 12:54:02 -05:00
192217a10c
r539: use --splice-flank=yes by default
...
In human/mouse, the GTr..yAG pattern occurs to 91/92% of all GT-AG introns.
Modeling r..y clearly leads to higher accuracy. However, in SIRV, this
percentage is reduced to ~60%. The default "--splice --splice-flank=yes"
leads to lower accuracy. If someone benchmark minimap2 on SIRV, this would be
bad, but minimap2 is developed for practical applications, not for benchmarks.
I will live with that.
2017-10-28 22:29:55 -04:00
Heng Li