Heng Li
|
55e39c2d30
|
r921: output unmapped reads in full PAF
|
2019-02-27 15:03:19 -05:00 |
Kevin Chan
|
90b7b83ec7
|
fix typo in command line help
|
2019-02-27 14:46:57 -05:00 |
|
Heng Li
|
d431dc0181
|
r917: added --max-chain-iter to avoid worst case
Resolves #324
|
2019-02-27 14:41:01 -05:00 |
|
Heng Li
|
ccf1680aaf
|
make it explicit that -x is preferred for prebuilt
|
2019-02-27 12:43:33 -05:00 |
|
Heng Li
|
ea84fc0a53
|
r917: fixed a bug in command-line parsing
Resolves #344
|
2019-02-27 11:22:58 -05:00 |
|
Heng Li
|
19208fb06b
|
r916: support long cs in sam-to-paf conversion
|
2019-02-17 09:35:23 -05:00 |
|
Heng Li
|
e02bebd96d
|
r915: fixed a bug caused by the latest change
|
2019-02-14 10:04:04 -05:00 |
|
Heng Li
|
32ab6ce15b
|
r914: fixed two harmless division by 0
Resolves #326
|
2019-02-12 19:30:49 -05:00 |
|
Heng Li
|
1739a260fb
|
r913: output tag "rl", length of unseedable regs
|
2019-02-05 14:19:17 -05:00 |
|
Heng Li
|
aaf3233818
|
added mappy.Aligner.seq_names to return seq names
Resolves #312
|
2019-01-29 12:53:20 -05:00 |
|
Heng Li
|
8b05880f73
|
r911: option -o to output to file (#319)
|
2019-01-29 10:42:20 -05:00 |
|
Heng Li
|
eba237f39d
|
r910: meaningful error message (#320)
when minimap2 fails to create temporary files
|
2019-01-29 10:29:27 -05:00 |
|
Heng Li
|
a8e1e3cbb8
|
updated citation with page numbers
|
2019-01-26 17:59:36 -05:00 |
|
Heng Li
|
597212b9f3
|
r908: added an assertion to detect a potential bug
as in #311
|
2019-01-23 11:18:50 -05:00 |
|
Heng Li
|
30abcf3cf9
|
r907: copy tag "cs" in sam2paf
Resolves #310
|
2019-01-13 17:52:31 -05:00 |
|
Heng Li
|
48e230f40d
|
r906: de tag is wrongly calculated given "N"
Resolves #309
|
2019-01-11 19:39:09 -05:00 |
|
Heng Li
|
c404f49569
|
Release minimap2-2.15 (r905)
|
2019-01-10 12:34:45 -05:00 |
|
Heng Li
|
cf2bae6e9b
|
r904: fixed a corner-case segfault. Resolves #307.
|
2019-01-10 09:57:05 -05:00 |
|
Heng Li
|
5b2fdfff9c
|
r895: option in asmgene to count autosomal only
|
2018-12-14 10:36:47 -05:00 |
|
Heng Li
|
ea2b1c5b2a
|
r894: added --max-qlen to filter out long query
|
2018-12-12 12:27:32 -05:00 |
|
Heng Li
|
eef1cee9b7
|
r893: added paftools.js vcfpair
|
2018-12-01 18:53:03 -05:00 |
|
Heng Li
|
2c52364527
|
r892: avoid de:f:0.0000
|
2018-11-24 21:54:28 -05:00 |
|
Heng Li
|
128476efc9
|
r891: compute gap-compressed divergence
|
2018-11-24 21:50:49 -05:00 |
|
Heng Li
|
1b3a6a0fe5
|
r890: removed "register" (#261)
|
2018-11-19 13:57:31 -05:00 |
|
Heng Li
|
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 |
|
Heng Li
|
62bbadf668
|
r887: fixed a bug in asmgene
|
2018-11-11 21:35:19 -05:00 |
|
Heng Li
|
91f548b497
|
r886: fixed two minor typos
Resolves #264
Resolves #265
|
2018-11-08 12:04:14 -05:00 |
|
Heng Li
|
cdaf46665a
|
r885: compute dup with asmstat
|
2018-11-07 00:26:05 -05:00 |
|
Heng Li
|
6596c63dcd
|
r884: for C++ compatibility (#261)
|
2018-11-06 22:07:11 -05:00 |
|
Heng Li
|
59f23f7579
|
Release minimap2-2.14 (r883)
|
2018-11-06 00:03:16 -05:00 |
|
Heng Li
|
5e55e397e9
|
r882: guard against -E0 (#263)
|
2018-11-05 23:36:12 -05:00 |
|
Heng Li
|
88c421e8de
|
r881: a recent change reduces sr accuracy
|
2018-11-05 22:03:59 -05:00 |
|
Heng Li
|
3db5bfe6e5
|
r880: fixed false wrong FASTA/Q alert
|
2018-11-05 20:52:07 -05:00 |
|
Heng Li
|
83dfdd5f50
|
draft release note
|
2018-11-05 20:07:57 -05:00 |
|
Heng Li
|
8a2b1cd4c9
|
updated mappy for extra option max_sw_mat
|
2018-11-05 19:28:44 -05:00 |
|
Heng Li
|
1ede8ca170
|
r877: renamed cap-sw-mat to cap-sw-mem
|
2018-11-05 11:46:38 -05:00 |
|
Heng Li
|
13981404e2
|
r876: skip DP if taking too much RAM (#259)
|
2018-11-05 11:43:10 -05:00 |
|
Heng Li
|
fd64dd26f6
|
r875: warn given incorrect FASTA/Q
resolves #252
resolves #255
|
2018-11-05 10:02:44 -05:00 |
|
Heng Li
|
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 |
|
Heng Li
|
a8ee48c2ce
|
r873: comforming to C99/C11; resolves #261
|
2018-11-05 08:25:07 -05:00 |
|
Heng Li
|
09e089c3dc
|
r872: choose the longest isoform
|
2018-11-04 23:48:50 -05:00 |
|
Heng Li
|
e46cbb7d84
|
r871: print erroneous genes
|
2018-11-04 20:37:06 -05:00 |
|
Heng Li
|
57ec73ec6c
|
r870: separate <50% and <10%
|
2018-11-04 19:31:25 -05:00 |
|
Heng Li
|
9e27575387
|
r869: classify incomplete genes
|
2018-11-04 19:21:55 -05:00 |
|
Heng Li
|
b4ad8d8bf0
|
added asmgene
improvements coming; not made public yet
|
2018-11-04 17:24:05 -05:00 |
|
Heng Li
|
e315b9fada
|
hidden options to control bp calculation
|
2018-11-04 16:36:04 -05:00 |
|
Heng Li
|
42baf287a4
|
r866: fixed a typo; resolves #262
|
2018-10-30 09:11:55 -04:00 |
|
Heng Li
|
2ceba22a7a
|
fixed a typo in manpage
|
2018-10-28 11:51:02 -04:00 |
|
Heng Li
|
9ed56b4a25
|
r860: MD/cs not working with --eqx
|
2018-10-26 23:23:53 -04:00 |
|
Heng Li
|
ecb6c5c36c
|
Document --no-pairing (#256)
|
2018-10-23 10:00:21 -04:00 |