64c1389e1a
Merge branch 'master' into splice
2017-08-17 23:39:27 +08:00
81cff97208
r299: support -h: output to stdout; return 0
2017-08-17 23:38:31 +08:00
bbb37d95f2
support inserting RG lines
2017-08-17 23:34:09 +08:00
2cde8d257c
r297: bidirectional RNA alignment
2017-08-17 06:02:44 -04:00
b5f5929bf9
r296: expose splicing related options to CLI
2017-08-13 21:37:51 -04:00
28f86688ab
r295: gap closure from the middle of non-HPC k
...
This WILL slightly affect the result of genomic mapping, but hopefully
in the good direction.
2017-08-12 23:48:43 -04:00
43506edbc5
backup: preliminary boundary alignment
2017-08-12 23:10:14 -04:00
bcfe00d2ad
minor formatting changes
2017-08-12 19:09:33 -04:00
17c19e5819
exts2 working
2017-08-12 19:06:59 -04:00
61eef0575c
separate out spliced alignment; not right yet
2017-08-12 18:54:32 -04:00
53b3265d84
r290: in techrep, explain spliced alignment
2017-08-12 15:40:49 -04:00
a23df2dc91
r289: changed CLI help only
2017-08-12 12:40:07 -04:00
5a74088b74
r288: changed max intron length to 200k
2017-08-12 12:39:21 -04:00
d240318741
r287: refined CLI options and manpage
2017-08-12 12:26:04 -04:00
0f4c823b0c
r286: ignore introns when computing max seg score
2017-08-12 10:58:16 -04:00
2d11aaa830
option to print all exons for debugging
2017-08-12 10:04:16 -04:00
30b8cb4672
option to print correct exons
2017-08-11 17:50:21 -04:00
0c1760bc86
bugfix; print errors; better rules
2017-08-11 16:28:52 -04:00
a99358bc3d
r282: reduced intron cost; added eval script
2017-08-11 00:06:01 -04:00
163fa36ee6
r281: don't open long gaps on query
2017-08-10 15:04:59 -04:00
c59b0781bc
r280: output introns as "N" in the cdna mode
2017-08-09 11:45:02 -04:00
7429b12164
Merge branch 'master' into cdna
2017-08-08 22:00:24 -04:00
9e1125edda
r277: abort if query/-d missing ( #11 )
2017-08-08 21:46:15 -04:00
4db0d1034b
Show travis CI status
2017-08-08 21:32:56 -04:00
3dbe23b34e
Merge branch 'dev'
2017-08-08 21:30:32 -04:00
6840370f3c
Release minimap2-2.0 (r275)
2017-08-08 21:16:25 -04:00
7f9f659b6a
r274: CLI option to change max ref gap
2017-08-08 11:39:23 -04:00
1a7d782131
r273: cdna mapping mode for testing
...
Differences from the typical mapping mode:
* banded alignment disabled
* log gap cost during chaining
* zero long-gap extension during alignment
* up to 100kb (by default) reference gap
* bad seeding not filtered (to tune later)
2017-08-08 11:31:49 -04:00
4badf2fcbf
avoid wasted memory allocation for backtrack
2017-08-08 11:29:46 -04:00
0137d0dfab
command lines used for read simulation
2017-08-07 13:41:40 -04:00
5b10667967
sim-eval.js to support mason2 read names and SAM
2017-08-07 13:28:33 -04:00
bd1541dce1
renamed simulation-related scripts
2017-08-07 13:26:25 -04:00
1597f2b030
convert mason2 SAM to fastq
2017-08-07 12:45:34 -04:00
ce927d2aee
Merge branch 'master' into dev
2017-08-07 12:44:07 -04:00
8c2917b391
Added citation.
2017-08-06 21:30:47 -04:00
9fcf8b6315
added basic travis CI
2017-08-04 15:33:40 -04:00
3217178d4a
fixed k8 download page
2017-08-04 14:53:00 -04:00
b40598fa91
added paf2aln.js example
2017-08-04 14:51:33 -04:00
269b8661b9
minor clarification
2017-08-04 14:49:25 -04:00
890d7bbd5b
added README for misc scripts
2017-08-04 14:46:31 -04:00
1aca0d5098
copied sam2paf.js here for completeness
2017-08-04 14:44:37 -04:00
68d99f0edb
Merge branch 'cs-tag' into dev
2017-08-04 14:31:46 -04:00
fd66ab5413
blast-like output working
2017-08-04 14:31:21 -04:00
71f82759af
convert paf to maf
2017-08-04 13:05:46 -04:00
648cdd8a3b
minor wording changes
2017-08-04 10:21:10 -04:00
7e231cfd3a
minor wording improvement
2017-08-03 21:28:01 -04:00
95d3c30ae3
rephrasing a bit to avoid the apparent TeX bug
...
Several hours sank into this. Damned...
2017-08-03 20:19:00 -04:00
f57fd8c790
added one transition phrase
...
as there are no subsubsections now
2017-08-03 18:01:48 -04:00
c70b20ee6d
removed subsubsection
...
TeX Live 2016 doesn't work with section and content on the same line.
2017-08-03 17:58:36 -04:00
e8d00a8c8c
removed trailing ^M
2017-08-03 17:20:43 -04:00
Heng Li