Heng Li
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7ef5490884
|
r703: added --max-clip-ratio
still testing the option
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2018-02-12 13:29:18 -05:00 |
|
Heng Li
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f66de7df59
|
updated paftools revision number to r702
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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
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6e65c5e631
|
Revision 1
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2018-02-09 17:39:02 -05:00 |
|
Heng Li
|
a58b05a61b
|
extend the section on genome alignment
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2018-02-09 13:59:00 -05:00 |
|
Heng Li
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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
|
01560f1db0
|
Revision v1, to be submitted
|
2018-02-07 11:07:08 -05:00 |
|
Heng Li
|
39535565ee
|
first round of revision
|
2018-02-06 16:19:22 -05:00 |
|
Heng Li
|
a8d476c6ad
|
r686: end seed trimming don't go over long join
|
2018-02-06 11:31:32 -05:00 |
|
Heng Li
|
29b4a1786c
|
r685: tune end seed filter again
|
2018-02-05 11:48:22 -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
|
35d3e064bf
|
r677: reduce the change of missing hits
that are close to end of alignments. It is still possible to create examples
that fail the heuristic.
|
2018-02-02 10:35:33 -05:00 |
|
Heng Li
|
997ab9bb2e
|
Fixed the description of --dual
|
2018-02-01 15:11:51 -05:00 |
|
Heng Li
|
53ce317e59
|
Release minimap2-2.8 (r672)
|
2018-02-01 12:50:20 -05:00 |
|
Heng Li
|
da6947cfa3
|
r671: cleanup command line options
|
2018-01-31 13:59:52 -05:00 |
|
Heng Li
|
46d6349af4
|
r670: added PE support to mappy
and minor code cleanup
|
2018-01-31 11:33:08 -05:00 |
|
Heng Li
|
12a5a5fa3c
|
r669: improved self chain extension (#10)
This has not fully resolved #10, only alleviated the issue.
|
2018-01-30 20:05:02 -05:00 |
|
Heng Li
|
ad18fa490d
|
fixed typos
|
2018-01-30 10:11:50 -05:00 |
|
Heng Li
|
43bfa6199d
|
r667: warn if one query file has fewer records #92
|
2018-01-28 17:36:21 -05:00 |
|
Heng Li
|
72b9b0e3b6
|
r666: report if >=3 query files in SR mode #92
|
2018-01-28 17:15:57 -05:00 |
|
Heng Li
|
6205fa6f21
|
document --heap-sort
|
2018-01-26 15:15:40 -05:00 |
|
Heng Li
|
d676a5314b
|
r664: use --heat-sort for sr by default
|
2018-01-26 12:25:42 -05:00 |
|
Heng Li
|
dfc78b39d3
|
refactor the old sorting
|
2018-01-26 09:37:48 -05:00 |
|
Heng Li
|
7b57c9a619
|
heap sort working on MT
|
2018-01-26 09:21:45 -05:00 |
|
Heng Li
|
123bc1d91d
|
put option operations in another file
|
2018-01-26 08:38:37 -05:00 |
|
Heng Li
|
dd18307e66
|
code backup
|
2018-01-25 21:52:49 -05:00 |
|
Heng Li
|
543fa12e68
|
r659: for C++ compatibility
|
2018-01-19 10:40:18 -05:00 |
|
Heng Li
|
af1a871270
|
r658: gives a warning if -N0 is used
|
2018-01-19 08:33:20 -05:00 |
|
Heng Li
|
2b71181a37
|
r657: check -p (#96)
Well, in principle, every option should be checked. Will do when someone raise
issues...
|
2018-01-19 01:03:38 -05:00 |
|
Heng Li
|
0454e6be91
|
explain -M in the manpage
|
2018-01-18 11:47:11 -05:00 |
|
Heng Li
|
33f8157961
|
r655: options to map to one strand of the ref #91
|
2018-01-16 10:34:30 -05:00 |
|
Heng Li
|
eecc06086f
|
Released minimap2-2.7 (r654)
|
2018-01-09 13:16:00 -05:00 |
|
Heng Li
|
dfea113f28
|
r653: the last change may write "N" wrongly
|
2018-01-08 11:33:53 -05:00 |
|
Heng Li
|
1842d7f5b5
|
allow to exclude regions
|
2018-01-07 22:35:56 -05:00 |
|
Heng Li
|
f5cfd439ee
|
r651: incorrectly treat introns as deletions
This happened when the last operation during backtracking is an intron.
|
2018-01-07 19:42:50 -05:00 |
|
Heng Li
|
248b43cc47
|
work with targets in BED12
|
2018-01-07 19:39:25 -05:00 |