Heng Li
|
194b457e79
|
option to print errors only
|
2021-02-07 12:58:03 -05:00 |
|
Heng Li
|
75c8933511
|
evaluate large-scale misjoins
|
2021-02-07 12:34:13 -05:00 |
|
Heng Li
|
1025993469
|
print number of errors on each read
|
2021-01-29 14:08:21 -05:00 |
|
Heng Li
|
a3253d1a6b
|
added a command for simple VCF statistics
|
2021-01-14 12:24:38 -05:00 |
|
Heng Li
|
29f67a1666
|
r982: more accurate sum; output errors
|
2020-04-14 16:18:53 -04:00 |
|
Heng Li
|
f10dff78dc
|
r981: asmgene to check duplicate genes
|
2020-04-14 15:52:36 -04:00 |
|
Heng Li
|
50775362bb
|
r980: support auNGA
|
2020-04-10 21:36:59 -04:00 |
|
Heng Li
|
0a5e386359
|
r979: fixed asmgene wrong report. Resolves #581.
|
2020-04-06 19:57:15 -04:00 |
|
Heng Li
|
e2451e497a
|
r975: asmstat without CIGAR/NM
|
2020-03-22 19:16:43 -04:00 |
|
Heng Li
|
58c2251b18
|
compatibility with GenBank GTP (resolves $422)
|
2019-06-11 09:16:03 -04:00 |
|
Heng Li
|
7bc87b4175
|
Release minimap2-2.17 (r941)
|
2019-05-04 23:49:17 -04:00 |
|
Heng Li
|
f64e426a5a
|
r933: resume versioning
|
2019-04-28 17:05:37 -04:00 |
|
Heng Li
|
cdc730d573
|
gff2bed to output junction BED
|
2019-04-28 16:47:12 -04:00 |
|
Heng Li
|
6b391e3373
|
Release minimap2-2.16 (r922)
|
2019-02-28 15:49:24 -05:00 |
|
Heng Li
|
55e39c2d30
|
r921: output unmapped reads in full PAF
|
2019-02-27 15:03:19 -05:00 |
|
Heng Li
|
19208fb06b
|
r916: support long cs in sam-to-paf conversion
|
2019-02-17 09:35:23 -05:00 |
|
Heng Li
|
30abcf3cf9
|
r907: copy tag "cs" in sam2paf
Resolves #310
|
2019-01-13 17:52:31 -05:00 |
|
Heng Li
|
c404f49569
|
Release minimap2-2.15 (r905)
|
2019-01-10 12:34:45 -05:00 |
|
Heng Li
|
5b2fdfff9c
|
r895: option in asmgene to count autosomal only
|
2018-12-14 10:36:47 -05:00 |
|
Heng Li
|
eef1cee9b7
|
r893: added paftools.js vcfpair
|
2018-12-01 18:53:03 -05:00 |
|
Heng Li
|
62bbadf668
|
r887: fixed a bug in asmgene
|
2018-11-11 21:35:19 -05:00 |
|
Heng Li
|
cdaf46665a
|
r885: compute dup with asmstat
|
2018-11-07 00:26:05 -05:00 |
|
Heng Li
|
59f23f7579
|
Release minimap2-2.14 (r883)
|
2018-11-06 00:03:16 -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
|
5d5d392c02
|
Release minimap2-2.13 (r850)
|
2018-10-11 13:18:31 -04:00 |
Torsten Seemann
|
34be359e25
|
Add -s sample option for VCF output
|
2018-09-19 18:24:47 -04:00 |
|
Heng Li
|
5cfa621b2d
|
use unmapped records
|
2018-07-07 12:49:15 -05:00 |
|
Heng Li
|
bcf92b3c46
|
compute query coverage
|
2018-07-06 21:52:01 -05:00 |
|
Heng Li
|
097378ab90
|
reworked break point counting
|
2018-07-06 09:46:26 -04:00 |
|
Heng Li
|
10bbbe28c5
|
added asmstat
|
2018-07-05 13:22:32 -04:00 |
|
Heng Li
|
50dae10421
|
paftools call to show statistics on longer indels
|
2018-07-03 14:28:09 -04:00 |
|
Heng Li
|
39f836eac8
|
r767: don't crash when there is no "cg" (#153)
|
2018-04-24 12:32:37 -04:00 |
apregier
|
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 |
|
Heng Li
|
0bf97a367b
|
r755: junceval to only evaluate chromosomes
|
2018-03-24 23:10:06 -04:00 |
|
Heng Li
|
1c504d72e4
|
r754: option to only change name
|
2018-03-23 12:27:11 -04:00 |
|
Heng Li
|
242ff4e91d
|
r745: junceval - recognize "-" as file name
|
2018-03-15 12:51:46 -04:00 |
|
Heng Li
|
77ebd479f4
|
r743: added VCF output to "call"
|
2018-03-12 21:51:31 -04:00 |
|
Heng Li
|
ccaf12e1a2
|
r734: removed debugging print in call()
|
2018-03-09 23:46:21 -05:00 |
|
Heng Li
|
70428ca3a8
|
speedup tag parsing for sam2paf
|
2018-03-02 10:17:55 -05:00 |
|
Heng Li
|
9aea79d621
|
faster tag parsing
|
2018-03-02 10:09:14 -05:00 |
|
Heng Li
|
1770988627
|
make calling work with sam2paf output
|
2018-03-02 10:03:06 -05:00 |
|
Heng Li
|
2bfdad34bb
|
minor cleanup to last commit
|
2018-03-02 01:07:37 -05:00 |
|
Heng Li
|
953766cedd
|
generate cs; not carefully tested
|
2018-03-02 00:14:55 -05:00 |
|
Heng Li
|
dc61301d9f
|
sam2paf cleanup
|
2018-03-01 21:58:12 -05:00 |
|
Heng Li
|
e1f18690f6
|
paftools-r713: fixed bug for cov1 regions
|
2018-02-16 12:20:46 -05:00 |