Heng Li
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1842d7f5b5
|
allow to exclude regions
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2018-01-07 22:35:56 -05:00 |
|
Heng Li
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248b43cc47
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work with targets in BED12
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2018-01-07 19:39:25 -05:00 |
|
Heng Li
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bf72969ab1
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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 |
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Heng Li
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7b5a601d48
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support paired-end reads
this gives unnecessary warnings, which will be fixed later.
|
2018-01-07 13:53:26 -05:00 |
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Heng Li
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e9607fcd9b
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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
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a465a920ec
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bug in block starts; added color and short-name
|
2018-01-05 21:45:56 -05:00 |
|
Heng Li
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b20839be77
|
more robust ID conversion
|
2018-01-05 17:55:24 -05:00 |
|
Heng Li
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209beb9955
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convert EnsEMBL to UCSC name (optional)
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2018-01-05 17:41:18 -05:00 |
|
Heng Li
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cfe87f50c1
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convert GTF/GFF3 to BED12
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2018-01-05 17:10:43 -05:00 |
|
Heng Li
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3a375d3436
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renamed paf2ovlp to ov-eval
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2017-12-24 18:04:00 -05:00 |
|
Heng Li
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626f10e0d0
|
evaluate sensitivity in the same script
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2017-12-24 17:55:42 -05:00 |
|
Heng Li
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b997578078
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find reads overlaps based on reference alignment
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2017-12-24 17:20:27 -05:00 |
|
Heng Li
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76206f574f
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support both SAM and PAF as input
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2017-12-02 21:57:19 -05:00 |
|
Heng Li
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e575f884e1
|
convert spliced PAF to BED
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2017-12-02 21:23:41 -05:00 |
|
Heng Li
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cbdb6c069f
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when there are incorrect anno, warn but not abort
|
2017-11-24 12:48:49 -05:00 |
|
Heng Li
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39a9666246
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convert PAF to LAST's cigar output
also added the support of BLAST-like output for "--cs=short".
|
2017-11-18 20:30:44 -05:00 |
|
Heng Li
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662d05dc02
|
fixed incorrect var coordinate
|
2017-11-12 20:25:33 -05:00 |
|
Heng Li
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379457c18b
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use mapq threshold
|
2017-11-12 19:01:34 -05:00 |
|
Heng Li
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03169d590b
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print cov-1 regions (not BED output any more)
|
2017-11-12 18:45:49 -05:00 |
|
Heng Li
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8c8d446820
|
find regions covered by one contig
|
2017-11-12 18:41:01 -05:00 |
|
Heng Li
|
0ddb064f17
|
dnadiff-like script; improvement coming
|
2017-11-12 15:07:29 -05:00 |
|
Heng Li
|
a13691d00d
|
eval script works with /[12] in SAM
|
2017-09-27 23:33:59 -04:00 |
|
Heng Li
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92ec8bd859
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added the /1 or /2 suffix
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2017-09-26 12:04:35 -04:00 |
|
Heng Li
|
6a82a21dee
|
r361: improved mapq for short reads
|
2017-09-13 15:32:39 -04:00 |
|
Heng Li
|
240f6caaff
|
backup manuscript
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2017-08-24 22:05:14 +08:00 |
|
Heng Li
|
ce859dbe1c
|
evaluate introns
this simplies the metrics
|
2017-08-20 21:54:59 +08:00 |
|
Heng Li
|
a4c41f64a5
|
the final version
to be replaced by intron-eval
|
2017-08-20 21:54:35 +08:00 |
|
Heng Li
|
5ed2faf270
|
minor tuning to the matching rules
|
2017-08-19 16:21:49 +08:00 |
|
Heng Li
|
2d11aaa830
|
option to print all exons for debugging
|
2017-08-12 10:04:16 -04:00 |
|
Heng Li
|
30b8cb4672
|
option to print correct exons
|
2017-08-11 17:50:21 -04:00 |
|
Heng Li
|
0c1760bc86
|
bugfix; print errors; better rules
|
2017-08-11 16:28:52 -04:00 |
|
Heng Li
|
a99358bc3d
|
r282: reduced intron cost; added eval script
|
2017-08-11 00:06:01 -04:00 |
|
Heng Li
|
5b10667967
|
sim-eval.js to support mason2 read names and SAM
|
2017-08-07 13:28:33 -04:00 |
|
Heng Li
|
bd1541dce1
|
renamed simulation-related scripts
|
2017-08-07 13:26:25 -04:00 |
|
Heng Li
|
1597f2b030
|
convert mason2 SAM to fastq
|
2017-08-07 12:45:34 -04:00 |
|
Heng Li
|
3217178d4a
|
fixed k8 download page
|
2017-08-04 14:53:00 -04:00 |
|
Heng Li
|
b40598fa91
|
added paf2aln.js example
|
2017-08-04 14:51:33 -04:00 |
|
Heng Li
|
269b8661b9
|
minor clarification
|
2017-08-04 14:49:25 -04:00 |
|
Heng Li
|
890d7bbd5b
|
added README for misc scripts
|
2017-08-04 14:46:31 -04:00 |
|
Heng Li
|
1aca0d5098
|
copied sam2paf.js here for completeness
|
2017-08-04 14:44:37 -04:00 |
|
Heng Li
|
68d99f0edb
|
Merge branch 'cs-tag' into dev
|
2017-08-04 14:31:46 -04:00 |
|
Heng Li
|
fd66ab5413
|
blast-like output working
|
2017-08-04 14:31:21 -04:00 |
|
Heng Li
|
71f82759af
|
convert paf to maf
|
2017-08-04 13:05:46 -04:00 |
|
Heng Li
|
8b1e36c609
|
minor tweaks to the evaluation script
|
2017-08-01 13:52:29 -04:00 |
|
Heng Li
|
ebbe9c1eb8
|
r219: fixed a bug caused by skipping tandem seeds
|
2017-07-28 14:06:56 -04:00 |
|
Heng Li
|
8b08a2ec41
|
added first-only and all-primary modes to eval
|
2017-07-26 19:32:26 -04:00 |
|
Heng Li
|
9f728dd96a
|
tunable overlap ratio
|
2017-07-26 18:30:29 -04:00 |
|
Heng Li
|
323293fbda
|
changed the way mapq is counted
|
2017-07-26 14:20:31 -04:00 |
|
Heng Li
|
bd33bed455
|
make output better
|
2017-07-26 12:03:42 -04:00 |
|
Heng Li
|
a8ad53ee81
|
evaluating read mapping for pbsim2fa reads
More functionality to be added later
|
2017-07-26 11:17:34 -04:00 |