Heng Li
|
f4a71d447f
|
Merge branch 'master' of github.com:lh3/minimap2
|
2017-09-03 11:07:32 -04:00 |
|
Heng Li
|
6db9b7579c
|
Better MSVC support
* get rid of alloca()
* no variable-sized arrays
|
2017-09-03 11:05:55 -04:00 |
|
Heng Li
|
f50b9a14a7
|
last commit can't be compiled
|
2017-09-02 21:07:19 -04:00 |
|
Heng Li
|
33423e1568
|
get rid of the last var-sized array in ksort
for MSVC
|
2017-09-02 21:05:03 -04:00 |
|
Heng Li
|
aeb6b5eeb1
|
fixed an issue due to the 64-bit assumption
|
2017-09-02 19:29:52 -04:00 |
|
Heng Li
|
3d3fde8224
|
replaced remaining alloca()
|
2017-09-02 18:50:42 -04:00 |
|
Heng Li
|
6f4cbf4f12
|
ok, %zu is a C99 feature...
|
2017-09-02 18:48:14 -04:00 |
|
Heng Li
|
2a5d5b6f12
|
print size_t with %zu instead of %lu
|
2017-09-02 18:37:48 -04:00 |
|
Heng Li
|
3d48516885
|
reduced a heap allocation
which *might* be frequent for short reads
|
2017-09-02 18:32:45 -04:00 |
|
Heng Li
|
00416c76d1
|
for MinGW32 compatibility
get rid of alloca()
|
2017-09-02 18:23:29 -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
|
c4080aaf7e
|
Merge branch 'master' into short
|
2017-08-28 07:02:22 +08:00 |
|
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
|
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 |