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 )
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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
79b0caca95
r537: model the next base to GT/AG
...
[PMID:18688272] shows that the base following GT tends to be A or G (i.e. R) in
both human and yeast, and that the base preceeding AG tends to be C or T (i.e.
Y). In the new model, we pay no cost to GTr..yAG, but we pay half of the cost
if there is no r or y. This improves the junction accuracy when mapping to
human and mouse and decreases the accuacy when mapping to SIRV. My guess is
that SIRV does not honor this trend. Need to investigate in future.
Also in this commit, --cost-non-gt-ag is aliased to -C. The default is changed
to 9 instead of 5. I also added --splice-flank to enable the above model. This
may become the default once I confirm my hypothesis on SIRV.
2017-10-28 00:25:01 -04:00
306e4541f8
Released minimap2-2.3 (r531)
2017-10-22 23:13:35 -04:00
04cf4ebf5e
r518: increased the default -K to 500M
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This helps multi-thread performance for ultra-long reads.
2017-10-17 13:21:29 -04:00
7c555f9b7e
r508: use two I/O threads for mapping
...
-x sr applies this option by default
2017-10-12 14:56:01 -04:00
Heng Li