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317 Commits 9 Branches 35 Tags
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Author SHA1 Message Date
Heng Li
6db9b7579c Better MSVC support 
* get rid of alloca()
* no variable-sized arrays
 2017-09-03 11:05:55 -04:00
Heng Li
2b8681ead7 fixed memory leak in example 2017-09-02 17:55:25 -04:00
Heng Li
0a3ebdc916 for better windows compatibility 2017-09-02 17:52:33 -04:00
Heng Li
b97620afed moved gettimeofday() to misc.c 2017-09-02 17:40:10 -04:00
Heng Li
743d26eab0 Merge pull request #20 from nanoporetech/msvc14 
ONT source code changes to compile with MSVC 14
 2017-09-02 14:35:02 -07:00
Heng Li
62535ecd7f Merge branch 'dev' 2017-09-01 10:06:21 -07:00
Heng Li
40665d1083 Merge pull request #23 from simonrharris/segfaultfix 
Fixed segfault caused when reading from index file
 2017-09-02 00:46:55 +08:00
Simon Harris
4db1c0295c Fixed segfault caused when reading from index file 2017-09-01 15:48:59 +01:00
Heng Li
d4074874ee r316: get rid of a harmless gcc warning 2017-09-01 20:25:27 +08:00
Heng Li
eccdb3a1ca r315: added getopt from musl 2017-09-01 20:20:34 +08:00
Stefan von Deylen
a3c3db6b9b ONT source code changes to compile with MSVC 14 2017-08-30 16:25:20 +01:00
Heng Li
2641613686 various minor improvements 2017-08-25 17:56:16 +08:00
Heng Li
5f96d851a8 added spliced alignment example 2017-08-25 14:11:54 +08:00
Heng Li
bf8246f872 Release minimap2-2.1-r311 v2.1 2017-08-25 13:35:55 +08:00
Heng Li
5cbd776651 test data for spliced alignment 2017-08-25 13:17:56 +08:00
Heng Li
0fe1a224ab r309: improved SAM header output 2017-08-25 10:35:58 +08:00
Heng Li
240f6caaff backup manuscript 2017-08-24 22:05:14 +08:00
Heng Li
b8bdac7e64 backup 2017-08-22 17:45:01 +08:00
Heng Li
19e4b2aab0 backup 2017-08-20 22:10:03 +08:00
Heng Li
ce859dbe1c evaluate introns 
this simplies the metrics
 2017-08-20 21:54:59 +08:00
Heng Li
a4c41f64a5 the final version 
to be replaced by intron-eval
 2017-08-20 21:54:35 +08:00
Heng Li
5ed2faf270 minor tuning to the matching rules 2017-08-19 16:21:49 +08:00
Heng Li
8058c85b72 moved appendix to methods; detailed splice aln 2017-08-18 23:33:57 +08:00
Heng Li
993a2bb521 r301: separate introns from deletions 
When an intron is adjacent to a deletion, the old code count both as introns,
which lead to an inaccurate exon boundary.
 2017-08-18 15:31:15 +08:00
Heng Li
64c1389e1a Merge branch 'master' into splice 2017-08-17 23:39:27 +08:00
Heng Li
81cff97208 r299: support -h: output to stdout; return 0 2017-08-17 23:38:31 +08:00
Heng Li
bbb37d95f2 support inserting RG lines 2017-08-17 23:34:09 +08:00
Heng Li
2cde8d257c r297: bidirectional RNA alignment 2017-08-17 06:02:44 -04:00
Heng Li
b5f5929bf9 r296: expose splicing related options to CLI 2017-08-13 21:37:51 -04:00
Heng Li
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
Heng Li
43506edbc5 backup: preliminary boundary alignment 2017-08-12 23:10:14 -04:00
Heng Li
bcfe00d2ad minor formatting changes 2017-08-12 19:09:33 -04:00
Heng Li
17c19e5819 exts2 working 2017-08-12 19:06:59 -04:00
Heng Li
61eef0575c separate out spliced alignment; not right yet 2017-08-12 18:54:32 -04:00
Heng Li
53b3265d84 r290: in techrep, explain spliced alignment 2017-08-12 15:40:49 -04:00
Heng Li
a23df2dc91 r289: changed CLI help only 2017-08-12 12:40:07 -04:00
Heng Li
5a74088b74 r288: changed max intron length to 200k 2017-08-12 12:39:21 -04:00
Heng Li
d240318741 r287: refined CLI options and manpage 2017-08-12 12:26:04 -04:00
Heng Li
0f4c823b0c r286: ignore introns when computing max seg score 2017-08-12 10:58:16 -04:00
Heng Li
2d11aaa830 option to print all exons for debugging 2017-08-12 10:04:16 -04:00
Heng Li
30b8cb4672 option to print correct exons 2017-08-11 17:50:21 -04:00
Heng Li
0c1760bc86 bugfix; print errors; better rules 2017-08-11 16:28:52 -04:00
Heng Li
a99358bc3d r282: reduced intron cost; added eval script 2017-08-11 00:06:01 -04:00
Heng Li
163fa36ee6 r281: don't open long gaps on query 2017-08-10 15:04:59 -04:00
Heng Li
c59b0781bc r280: output introns as "N" in the cdna mode 2017-08-09 11:45:02 -04:00
Heng Li
7429b12164 Merge branch 'master' into cdna 2017-08-08 22:00:24 -04:00
Heng Li
9e1125edda r277: abort if query/-d missing (#11) 2017-08-08 21:46:15 -04:00
Heng Li
4db0d1034b Show travis CI status 2017-08-08 21:32:56 -04:00
Heng Li
3dbe23b34e Merge branch 'dev' 2017-08-08 21:30:32 -04:00
Heng Li
6840370f3c Release minimap2-2.0 (r275) v2.0 2017-08-08 21:16:25 -04:00