08bd2123b6
r752: option to copy comments to output ( #136 )
2018-03-23 10:04:33 -04:00
8766d286df
r751: optionally output MD ( #118 )
2018-03-22 14:15:33 -04:00
623b5d9d48
r750: check puts() return ( #132 & #103 )
2018-03-22 11:31:58 -04:00
18659118cd
r749: don't print version etc at low verbose
2018-03-22 11:10:55 -04:00
d1050f4eaf
r748: optionally to use system getopt() ( #134 )
2018-03-19 11:18:26 -04:00
b81d45510e
Revision v2
2018-03-16 11:18:06 -04:00
d135feb1a5
response to reviewers' comments, round 2
2018-03-15 21:59:57 -04:00
242ff4e91d
r745: junceval - recognize "-" as file name
2018-03-15 12:51:46 -04:00
7a0c1316ce
added more examples to cookbook
2018-03-12 22:24:22 -04:00
77ebd479f4
r743: added VCF output to "call"
2018-03-12 21:51:31 -04:00
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
Heng Li