31fc0f218a
Allow setting max_frag_len parameter in Aligner class
2018-06-19 14:39:30 -04:00
3d3bcc29a8
Fix CIGAR reallocation with --eqx
...
Fix the logic that calculates the number of CIGAR entries when
match "M" entries are expanded into "=" and "X". The number
of entries depends not on the number of mismatches but rather
on the number of transitions between "=" to "X".
2018-06-19 14:37:41 -04:00
99dcd75f64
added support for 64 bit ARM architectures
2018-06-19 14:28:45 -04:00
154d2caf5b
r784: support the =/X CIGAR operators ( #156 )
2018-05-30 16:11:22 -04:00
a3afeec0b2
r783: reverted to r781 ( #155 )
2018-05-30 15:25:34 -04:00
3573784b4d
r782: no mask a chain having long ref ovlp ( #155 )
2018-05-30 13:53:45 -04:00
872f300955
r781: fixed the buggy heapmerge ( resolves #166 )
2018-05-30 11:55:14 -04:00
d7b61a039e
updated citation
2018-05-30 11:11:55 -04:00
248158a3e1
Resolved #168 : citing the manpage for cs
2018-05-30 11:03:16 -04:00
9f4309c376
r777: avoid skipping too many seeds
2018-05-11 10:25:18 -04:00
463f9309f9
Merge branch 'hot-fix' into fix-long-gap
2018-05-11 10:13:19 -04:00
abe989e355
the previous fix on int overflow is incomplete
2018-05-11 10:12:57 -04:00
881b4ca3a2
r774: Merge branch 'hot-fix' into fix-long-gap
2018-05-11 10:02:17 -04:00
10c6dd2551
r773: fixed an integer overflow
2018-05-11 10:01:23 -04:00
7ec6721c44
r772: option -Y not working
2018-05-11 10:00:11 -04:00
e61812ee55
reduced gap len to trigger bad seed filtering
2018-05-01 16:17:21 -04:00
734ac379bb
r770: matching N bases not working properly ( #155 )
2018-04-30 19:55:23 -04:00
759f8e4ac9
r769: filter out seeds breaking long gaps
2018-04-24 15:37:37 -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
39f836eac8
r767: don't crash when there is no "cg" ( #153 )
2018-04-24 12:32:37 -04:00
cbeb86dad6
Merge remote-tracking branch 'origin/master'
2018-04-10 09:12:26 -04:00
372c90ceb5
r764: fixed incorrect inversion mapq ( #148 )
2018-04-10 09:11:49 -04:00
2e2e69107c
Small bugfix for paftools.js
...
The bug resulted in the wrong coverage being printed in some cases.
2018-04-04 16:29:54 -04:00
ee4cd089f7
r763: fine control long join flank len ( #128 )
2018-03-29 14:16:58 -04:00
2d7ec75d50
Release minimap2-2.10 (r761)
2018-03-27 11:45:44 -04:00
7938ed4893
fixed two mappy warnings
2018-03-26 15:12:54 -04:00
4740423afa
Merge remote-tracking branch 'origin/master'
2018-03-26 14:37:17 -04:00
1776311a9b
updated cookbook
2018-03-26 14:37:02 -04:00
c1a3e05cb0
Merge pull request #138 from zingdle/patch-1
...
Fix typo in README.md
2018-03-26 07:50:39 -04:00
ecb6703d4a
Update README.md
...
Fix typo.
TD;DR -> TL;DR
2018-03-26 14:54:52 +08:00
0bf97a367b
r755: junceval to only evaluate chromosomes
2018-03-24 23:10:06 -04:00
1c504d72e4
r754: option to only change name
2018-03-23 12:27:11 -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
623b5d9d48
r750: check puts() return ( #132 & #103 )
2018-03-22 11:31:58 -04:00
18659118cd
r749: don't print version etc at low verbose
2018-03-22 11:10:55 -04:00
d1050f4eaf
r748: optionally to use system getopt() ( #134 )
2018-03-19 11:18:26 -04:00
b81d45510e
Revision v2
2018-03-16 11:18:06 -04:00
d135feb1a5
response to reviewers' comments, round 2
2018-03-15 21:59:57 -04:00
242ff4e91d
r745: junceval - recognize "-" as file name
2018-03-15 12:51:46 -04:00
7a0c1316ce
added more examples to cookbook
2018-03-12 22:24:22 -04:00
77ebd479f4
r743: added VCF output to "call"
2018-03-12 21:51:31 -04:00
e3f226a9d9
working on section "Full-Genome Alignment"
...
found an apparent bug in paftools.js call. To debug...
2018-03-12 16:12:18 -04:00
bdc615c1d4
r741: added --min-occ-floor to improve #107
2018-03-12 14:32:27 -04:00
ad1beaf255
backup; not finished
2018-03-12 13:20:25 -04:00
de0480ac5b
finished section "Read Overlap"
2018-03-12 13:05:51 -04:00
f2866533a8
finished "mapping genomic reads"
2018-03-12 12:50:21 -04:00
0173850ef0
don't use bullets - they are hard to read
2018-03-12 12:42:13 -04:00
acea3594fb
updated cookbook
2018-03-12 12:39:57 -04:00
mvdbeek
Aaron Wenger
Hasindu Gamaarachchi
Heng Li
apregier
zingdle