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
bdc615c1d4
r741: added --min-occ-floor to improve #107
2018-03-12 14:32:27 -04:00
ad1beaf255
backup; not finished
2018-03-12 13:20:25 -04:00
de0480ac5b
finished section "Read Overlap"
2018-03-12 13:05:51 -04:00
f2866533a8
finished "mapping genomic reads"
2018-03-12 12:50:21 -04:00
0173850ef0
don't use bullets - they are hard to read
2018-03-12 12:42:13 -04:00
acea3594fb
updated cookbook
2018-03-12 12:39:57 -04:00
f78a247749
Started to work on a cookbook
2018-03-12 12:00:44 -04:00
ccaf12e1a2
r734: removed debugging print in call()
2018-03-09 23:46:21 -05:00
96b132c97d
fixed a bug/typo in Aligner.seq() ( #126 )
2018-03-08 19:12:12 -05:00
70428ca3a8
speedup tag parsing for sam2paf
2018-03-02 10:17:55 -05:00
9aea79d621
faster tag parsing
2018-03-02 10:09:14 -05:00
1770988627
make calling work with sam2paf output
2018-03-02 10:03:06 -05:00
2bfdad34bb
minor cleanup to last commit
2018-03-02 01:07:37 -05:00
953766cedd
generate cs; not carefully tested
2018-03-02 00:14:55 -05:00
dc61301d9f
sam2paf cleanup
2018-03-01 21:58:12 -05:00
19e05a099d
for clarity
2018-03-01 18:25:29 -05:00
0238caa8b1
clarify minimap2 not working for >2Gbp seq #129
2018-03-01 18:23:40 -05:00
a22ebb9836
use SSE compiler flags more precisely ( #127 )
2018-02-26 09:51:01 -05:00
eeb314edd6
Release minimap2-2.9 (r720)
2018-02-24 09:31:09 -05:00
83c57a9d98
r719: fixed bad memory access
2018-02-23 17:27:41 -05:00
24a4808826
r718: retrieve sequence from the index
2018-02-23 10:18:26 -05:00
29ed675ee5
bugfix: in-place revcomp() not working
2018-02-20 11:05:54 -05:00
7dc7097208
added reverse complement
2018-02-20 09:41:25 -05:00
f434653432
added peakrss(); not used for now
2018-02-17 20:40:31 -05:00
090361c25b
fixed a typo in mappy ( #117 )
2018-02-16 21:10:57 -05:00
e1f18690f6
paftools-r713: fixed bug for cov1 regions
2018-02-16 12:20:46 -05:00
54a42aafe5
keep documents in sync
2018-02-15 17:21:09 -05:00
8fc5f8dc90
r711: assign proper mapq to primary inversions
2018-02-15 14:34:59 -05:00
a0d62519c1
r710: fixed incorrect inversion coordinate ( #112 )
2018-02-15 14:23:42 -05:00
b71c01b316
added test data for inversions
2018-02-15 11:04:27 -05:00
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
c0e0d5d84b
r707: bugfix for inversions on rev strand ( #112 )
2018-02-14 14:09:03 -05:00
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
3b17d62ccd
minor doc improvements
2018-02-12 22:27:02 -05:00
874b8c4795
rework misc/README; progressing but unfinished
2018-02-12 22:06:05 -05:00
7ef5490884
r703: added --max-clip-ratio
...
still testing the option
2018-02-12 13:29:18 -05:00
f66de7df59
updated paftools revision number to r702
2018-02-12 11:39:04 -05:00
fbbd4e0968
changed output messages for clarity
2018-02-12 11:32:32 -05:00
8c89ba005e
merged cnt-feat into paftools
2018-02-12 11:29:42 -05:00
50775a1e6f
added liftOver
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tested on a few toy examples
2018-02-12 11:12:23 -05:00
87cf650168
r697: fixed wrong #mapped reads in junceval
2018-02-09 18:45:57 -05:00
6e65c5e631
Revision 1
2018-02-09 17:39:02 -05:00
a58b05a61b
extend the section on genome alignment
2018-02-09 13:59:00 -05:00
42dab6319b
don't call SNPs involving 'n'
2018-02-09 13:27:17 -05:00
8428809369
convert MUMmer's delta to PAF
2018-02-09 12:14:28 -05:00
642af5591e
merged intron-eval into paftools
2018-02-09 11:07:14 -05:00
2025a6279a
merged gff2bed and mapstat to paftools
2018-02-09 10:47:12 -05:00
3465b04724
merged a few converters to paftools
2018-02-09 10:23:30 -05:00
66c5e71fa8
merging scripts into one long script
2018-02-09 10:00:35 -05:00
Heng Li