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Author SHA1 Message Date
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) v2.8 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) v2.7 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
a465a920ec bug in block starts; added color and short-name 2018-01-05 21:45:56 -05:00
Heng Li
b20839be77 more robust ID conversion 2018-01-05 17:55:24 -05:00
Heng Li
209beb9955 convert EnsEMBL to UCSC name (optional) 2018-01-05 17:41:18 -05:00
Heng Li
cfe87f50c1 convert GTF/GFF3 to BED12 2018-01-05 17:10:43 -05:00
Heng Li
680b971bb0 deleted duplicated entries 2018-01-01 19:52:21 -05:00
Heng Li
6b0d3c1fa8 added PHONY and comments to makefile 2017-12-30 20:54:11 -05:00
Heng Li
dc9e3dcf4a r639: changed -O/-E validation 2017-12-30 20:39:29 -05:00
Heng Li
cc75c12905 r638: disabled scoring checking 
I haven't figured out the exact bounds...
 2017-12-30 07:50:40 -05:00
Heng Li
f159e1c2d3 new section on HPC k-mers 2017-12-24 19:11:23 -05:00
Heng Li
3a375d3436 renamed paf2ovlp to ov-eval 2017-12-24 18:04:00 -05:00
Heng Li
626f10e0d0 evaluate sensitivity in the same script 2017-12-24 17:55:42 -05:00
Heng Li
b997578078 find reads overlaps based on reference alignment 2017-12-24 17:20:27 -05:00
Heng Li
ce8a48d715 fixed two minor typos in references 2017-12-24 13:14:47 -05:00
Heng Li
99879e9e75 a new section on estimating sequence divergence 2017-12-24 12:57:38 -05:00
Heng Li
c969d1a1ce updated direct RNA-seq results; cite syndip 
and a few minor changes
 2017-12-24 11:06:17 -05:00