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
...
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
01560f1db0
Revision v1, to be submitted
2018-02-07 11:07:08 -05:00
39535565ee
first round of revision
2018-02-06 16:19:22 -05:00
a8d476c6ad
r686: end seed trimming don't go over long join
2018-02-06 11:31:32 -05:00
29b4a1786c
r685: tune end seed filter again
2018-02-05 11:48:22 -05:00
dbf284b2d9
r684: separate end score from min_chain_score
2018-02-05 11:40:38 -05:00
3df5015668
General doc improvements
2018-02-02 21:45:46 -05:00
756379bf83
Documented paf2diff.js (more to come later)
2018-02-02 14:43:58 -05:00
41fd8a966a
Documented ov-eval.js
2018-02-02 14:18:18 -05:00
86e4933b1a
Added TOC
2018-02-02 14:12:30 -05:00
a633a744b6
more doc in misc
2018-02-02 14:07:17 -05:00
ddc31f57ba
Documented some k8 scripts; more coming
2018-02-02 13:57:08 -05:00
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
997ab9bb2e
Fixed the description of --dual
2018-02-01 15:11:51 -05:00
53ce317e59
Release minimap2-2.8 (r672)
2018-02-01 12:50:20 -05:00
da6947cfa3
r671: cleanup command line options
2018-01-31 13:59:52 -05:00
46d6349af4
r670: added PE support to mappy
...
and minor code cleanup
2018-01-31 11:33:08 -05:00
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