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 |
|
Heng Li
|
3b17d62ccd
|
minor doc improvements
|
2018-02-12 22:27:02 -05:00 |
|
Heng Li
|
874b8c4795
|
rework misc/README; progressing but unfinished
|
2018-02-12 22:06:05 -05:00 |
|
Heng Li
|
f66de7df59
|
updated paftools revision number to r702
|
2018-02-12 11:39:04 -05:00 |
|
Heng Li
|
fbbd4e0968
|
changed output messages for clarity
|
2018-02-12 11:32:32 -05:00 |
|
Heng Li
|
8c89ba005e
|
merged cnt-feat into paftools
|
2018-02-12 11:29:42 -05:00 |
|
Heng Li
|
50775a1e6f
|
added liftOver
tested on a few toy examples
|
2018-02-12 11:12:23 -05:00 |
|
Heng Li
|
87cf650168
|
r697: fixed wrong #mapped reads in junceval
|
2018-02-09 18:45:57 -05:00 |
|
Heng Li
|
42dab6319b
|
don't call SNPs involving 'n'
|
2018-02-09 13:27:17 -05:00 |
|
Heng Li
|
8428809369
|
convert MUMmer's delta to PAF
|
2018-02-09 12:14:28 -05:00 |
|
Heng Li
|
642af5591e
|
merged intron-eval into paftools
|
2018-02-09 11:07:14 -05:00 |
|
Heng Li
|
2025a6279a
|
merged gff2bed and mapstat to paftools
|
2018-02-09 10:47:12 -05:00 |
|
Heng Li
|
3465b04724
|
merged a few converters to paftools
|
2018-02-09 10:23:30 -05:00 |
|
Heng Li
|
66c5e71fa8
|
merging scripts into one long script
|
2018-02-09 10:00:35 -05:00 |
|
Heng Li
|
dbf284b2d9
|
r684: separate end score from min_chain_score
|
2018-02-05 11:40:38 -05:00 |
|
Heng Li
|
3df5015668
|
General doc improvements
|
2018-02-02 21:45:46 -05:00 |
|
Heng Li
|
756379bf83
|
Documented paf2diff.js (more to come later)
|
2018-02-02 14:43:58 -05:00 |
|
Heng Li
|
41fd8a966a
|
Documented ov-eval.js
|
2018-02-02 14:18:18 -05:00 |
|
Heng Li
|
86e4933b1a
|
Added TOC
|
2018-02-02 14:12:30 -05:00 |
|
Heng Li
|
a633a744b6
|
more doc in misc
|
2018-02-02 14:07:17 -05:00 |
|
Heng Li
|
ddc31f57ba
|
Documented some k8 scripts; more coming
|
2018-02-02 13:57:08 -05:00 |
|
Heng Li
|
ad18fa490d
|
fixed typos
|
2018-01-30 10:11:50 -05:00 |
|
Heng Li
|
1842d7f5b5
|
allow to exclude regions
|
2018-01-07 22:35:56 -05:00 |
|
Heng Li
|
248b43cc47
|
work with targets in BED12
|
2018-01-07 19:39:25 -05:00 |
|
Heng Li
|
bf72969ab1
|
added a bed counter
I know there are tools for this purpose, but they don't quite meet my exact
need.
|
2018-01-07 15:19:18 -05:00 |
|
Heng Li
|
7b5a601d48
|
support paired-end reads
this gives unnecessary warnings, which will be fixed later.
|
2018-01-07 13:53:26 -05:00 |
|
Heng Li
|
e9607fcd9b
|
allow to convert read names
ONT read names are just too long and too hard to compress
|
2018-01-05 22:05:15 -05:00 |
|
Heng Li
|
a465a920ec
|
bug in block starts; added color and short-name
|
2018-01-05 21:45:56 -05:00 |
|
Heng Li
|
b20839be77
|
more robust ID conversion
|
2018-01-05 17:55:24 -05:00 |
|
Heng Li
|
209beb9955
|
convert EnsEMBL to UCSC name (optional)
|
2018-01-05 17:41:18 -05:00 |
|
Heng Li
|
cfe87f50c1
|
convert GTF/GFF3 to BED12
|
2018-01-05 17:10:43 -05:00 |
|
Heng Li
|
3a375d3436
|
renamed paf2ovlp to ov-eval
|
2017-12-24 18:04:00 -05:00 |