2bb8cbbeef
updated manpage
2019-04-28 17:02:49 -04:00
e80759c97a
--junc-bed apparently working
...
Also fixed an issue with splice alignment in the reverse strand, though this
should have a very minor effect in practice.
2019-04-28 16:47:12 -04:00
f4c844b143
fixed a few simple bugs and leaks
2019-04-28 16:47:12 -04:00
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
cdc730d573
gff2bed to output junction BED
2019-04-28 16:47:12 -04:00
6420acca6d
BED I/O
2019-04-28 16:47:12 -04:00
371bc9513a
SAM TLEN should be 0 when either read is unmapped
...
this_rid/this_pos will be copied from r_prev(=r_next)'s values when this
read is unmapped (i.e., r is NULL). In this case, we can write RNEXT as
'=' but should not calculate TLEN from these placeholder values.
Similarly when the mate is unmapped (i.e., r_next is NULL).
Fixes #365 .
2019-04-05 09:36:46 -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
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
ccf1680aaf
make it explicit that -x is preferred for prebuilt
2019-02-27 12:43:33 -05:00
ea84fc0a53
r917: fixed a bug in command-line parsing
...
Resolves #344
2019-02-27 11:22:58 -05:00
19208fb06b
r916: support long cs in sam-to-paf conversion
2019-02-17 09:35:23 -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
aaf3233818
added mappy.Aligner.seq_names to return seq names
...
Resolves #312
2019-01-29 12:53:20 -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
a8e1e3cbb8
updated citation with page numbers
2019-01-26 17:59:36 -05:00
597212b9f3
r908: added an assertion to detect a potential bug
...
as in #311
2019-01-23 11:18:50 -05:00
30abcf3cf9
r907: copy tag "cs" in sam2paf
...
Resolves #310
2019-01-13 17:52:31 -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
5b2fdfff9c
r895: option in asmgene to count autosomal only
2018-12-14 10:36:47 -05:00
ea2b1c5b2a
r894: added --max-qlen to filter out long query
2018-12-12 12:27:32 -05:00
eef1cee9b7
r893: added paftools.js vcfpair
2018-12-01 18:53:03 -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
62bbadf668
r887: fixed a bug in asmgene
2018-11-11 21:35:19 -05:00
91f548b497
r886: fixed two minor typos
...
Resolves #264
Resolves #265
2018-11-08 12:04:14 -05:00
cdaf46665a
r885: compute dup with asmstat
2018-11-07 00:26:05 -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
83dfdd5f50
draft release note
2018-11-05 20:07:57 -05:00
8a2b1cd4c9
updated mappy for extra option max_sw_mat
2018-11-05 19:28:44 -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
09e089c3dc
r872: choose the longest isoform
2018-11-04 23:48:50 -05:00
Heng Li
John Marshall
Kevin Chan