Heng Li
08bd2123b6
r752: option to copy comments to output ( #136 )
2018-03-23 10:04:33 -04:00
Heng Li
8766d286df
r751: optionally output MD ( #118 )
2018-03-22 14:15:33 -04:00
Heng Li
623b5d9d48
r750: check puts() return ( #132 & #103 )
2018-03-22 11:31:58 -04:00
Heng Li
18659118cd
r749: don't print version etc at low verbose
2018-03-22 11:10:55 -04:00
Heng Li
d1050f4eaf
r748: optionally to use system getopt() ( #134 )
2018-03-19 11:18:26 -04:00
Heng Li
b81d45510e
Revision v2
2018-03-16 11:18:06 -04:00
Heng Li
d135feb1a5
response to reviewers' comments, round 2
2018-03-15 21:59:57 -04:00
Heng Li
242ff4e91d
r745: junceval - recognize "-" as file name
2018-03-15 12:51:46 -04:00
Heng Li
7a0c1316ce
added more examples to cookbook
2018-03-12 22:24:22 -04:00
Heng Li
77ebd479f4
r743: added VCF output to "call"
2018-03-12 21:51:31 -04:00
Heng Li
e3f226a9d9
working on section "Full-Genome Alignment"
...
found an apparent bug in paftools.js call. To debug...
2018-03-12 16:12:18 -04:00
Heng Li
bdc615c1d4
r741: added --min-occ-floor to improve #107
2018-03-12 14:32:27 -04:00
Heng Li
ad1beaf255
backup; not finished
2018-03-12 13:20:25 -04:00
Heng Li
de0480ac5b
finished section "Read Overlap"
2018-03-12 13:05:51 -04:00
Heng Li
f2866533a8
finished "mapping genomic reads"
2018-03-12 12:50:21 -04:00
Heng Li
0173850ef0
don't use bullets - they are hard to read
2018-03-12 12:42:13 -04:00
Heng Li
acea3594fb
updated cookbook
2018-03-12 12:39:57 -04:00
Heng Li
f78a247749
Started to work on a cookbook
2018-03-12 12:00:44 -04:00
Heng Li
ccaf12e1a2
r734: removed debugging print in call()
2018-03-09 23:46:21 -05:00
Heng Li
96b132c97d
fixed a bug/typo in Aligner.seq() ( #126 )
2018-03-08 19:12:12 -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
19e05a099d
for clarity
2018-03-01 18:25:29 -05:00
Heng Li
0238caa8b1
clarify minimap2 not working for >2Gbp seq #129
2018-03-01 18:23:40 -05:00
Heng Li
a22ebb9836
use SSE compiler flags more precisely ( #127 )
2018-02-26 09:51:01 -05:00
Heng Li
eeb314edd6
Release minimap2-2.9 (r720)
2018-02-24 09:31:09 -05:00
Heng Li
83c57a9d98
r719: fixed bad memory access
2018-02-23 17:27:41 -05:00
Heng Li
24a4808826
r718: retrieve sequence from the index
2018-02-23 10:18:26 -05:00
Heng Li
29ed675ee5
bugfix: in-place revcomp() not working
2018-02-20 11:05:54 -05:00
Heng Li
7dc7097208
added reverse complement
2018-02-20 09:41:25 -05:00
Heng Li
f434653432
added peakrss(); not used for now
2018-02-17 20:40:31 -05:00
Heng Li
090361c25b
fixed a typo in mappy ( #117 )
2018-02-16 21:10:57 -05:00
Heng Li
e1f18690f6
paftools-r713: fixed bug for cov1 regions
2018-02-16 12:20:46 -05:00
Heng Li
54a42aafe5
keep documents in sync
2018-02-15 17:21:09 -05:00
Heng Li
8fc5f8dc90
r711: assign proper mapq to primary inversions
2018-02-15 14:34:59 -05:00
Heng Li
a0d62519c1
r710: fixed incorrect inversion coordinate ( #112 )
2018-02-15 14:23:42 -05:00
Heng Li
b71c01b316
added test data for inversions
2018-02-15 11:04:27 -05:00
Heng Li
1372977a37
r708: implemented double Z-drop thresholds ( #112 )
...
When aligning long reads, we would prefer to align through low-quality
regions. This requires a large Z-drop threshold. However, to find small
inversions, we need to use a small Z-drop. This commit address this
conflict with two Z-drop thresholds. When Z-drop exceeds the smaller
threshold, we perform a local alignment to check if there is a potential
inversion. If there is one, we break the alignment; otherwise we break
the alignment only if Z-drop excess the larger threshold.
This commit also fixes a bug that reported wrong coordinates when the
inversion is on the forward strand (#112 ).
2018-02-15 10:50:49 -05:00
Heng Li
c0e0d5d84b
r707: bugfix for inversions on rev strand ( #112 )
2018-02-14 14:09:03 -05:00
Heng Li
b328795051
r706: don't segfault upon wrong FASTA/Q ( #111 )
...
The lack of robustness cost me several hours to identify.
2018-02-13 10:00:22 -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
7ef5490884
r703: added --max-clip-ratio
...
still testing the option
2018-02-12 13:29:18 -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
6e65c5e631
Revision 1
2018-02-09 17:39:02 -05:00
Heng Li
a58b05a61b
extend the section on genome alignment
2018-02-09 13:59:00 -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
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
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
405d531100
don't test python v3.3
2018-01-05 22:17:00 -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