f995f55610
added --mask-len for #659
2020-08-21 11:12:50 -04:00
ccb0f7b05d
added a new Makefile for simde
2020-04-25 22:43:29 -04:00
66db9da7d8
changed preprocessor conditionals for SIMDe
2020-04-22 19:50:59 +02:00
2b3403f094
fix for Neon after test.
2020-04-21 02:08:21 +02:00
3e16e4e39d
Added documentation entry for added functionality, simde and no_simd.
2020-04-21 01:36:19 +02:00
f47e8a525e
SIMDe made optional. Include paths changes for SIMDe.
2020-04-21 01:08:32 +02:00
c172df7d2d
fix for Neon
2020-04-20 21:14:15 +02:00
9e6fdd376b
Changed sse2neon with SIMDe. Added building non-SIMD version.
2020-04-20 18:28:06 +02:00
29f67a1666
r982: more accurate sum; output errors
2020-04-14 16:18:53 -04:00
adde608a42
Merge remote-tracking branch 'refs/remotes/origin/master'
2020-04-14 15:52:57 -04:00
f10dff78dc
r981: asmgene to check duplicate genes
2020-04-14 15:52:36 -04:00
d97bba9f27
travis: added arm64 test.
2020-04-13 08:33:03 -04:00
50775362bb
r980: support auNGA
2020-04-10 21:36:59 -04:00
0a5e386359
r979: fixed asmgene wrong report. Resolves #581 .
2020-04-06 19:57:15 -04:00
cb56fb762a
Merge branch 'master' of github.com:lh3/minimap2
2020-03-22 19:17:01 -04:00
e2451e497a
r975: asmstat without CIGAR/NM
2020-03-22 19:16:43 -04:00
d2de282d21
remove second definition of kstring
2020-03-02 13:18:37 -05:00
48cb80ea94
change kstring_t integer storage size
...
This is for compatibility with kstring_t in htslib.
2020-02-28 09:35:51 -05:00
6a4b9f9082
r974: more informative msg on wrong FASTQ records
...
Resolves #510
2020-01-21 10:56:59 -05:00
a7a01fe5bd
r973: fixed compiling errors caused
2020-01-21 10:43:31 -05:00
9dceae59a0
r972: renamed --alt-diff to --alt-drop
2020-01-21 10:33:39 -05:00
20a3987082
Merge branch 'master' into alt
2020-01-21 09:17:50 -05:00
eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -05:00
7996f04008
r972: fixed negative de:f caused by ambiguous base
2020-01-21 09:14:37 -05:00
d2e14705e7
r968: allow large mini_batch; resolves #491
2020-01-18 12:24:44 -05:00
24f50f38e8
r967: no duplicated @SQ lines with --split-prefix
...
resolves #527 and #400
2020-01-18 12:01:28 -05:00
04e015d803
r966: minimap2 returns 1 on file failure ( #532 )
2020-01-18 10:58:59 -05:00
040f74102c
r965: added --chain-gap-scale for #540
2020-01-18 10:29:33 -05:00
cdb7857841
r963: --junc-bonus not working; resolves #513
2020-01-06 22:03:50 -05:00
3c0d05d272
r962: abort given wrong RG line; resolves #541
2020-01-06 21:53:21 -05:00
47b646acbf
r961: print indexed length
2020-01-06 21:13:33 -05:00
a79cb3e991
Merge remote-tracking branch 'origin/master'
2019-12-23 17:33:56 -05:00
367aed4271
added the asan and tsan targets to Makefile
2019-12-23 17:33:10 -05:00
081df6ac7d
Fix example.c seq read logic
...
for every idx should map all input seqs
2019-11-11 00:46:07 -05:00
a3e7a575fb
Add splice:hq to --help
2019-11-11 00:45:13 -05:00
d90583b83c
r954: fixed two potential undef behaviors ( #443 )
2019-07-18 09:17:08 -04:00
7fc03b0c32
r953: krealloc is buggy
...
Its use in minimap2 didn't trigger the bug, so the older minimap2 is still ok.
2019-07-18 09:13:30 -04:00
20c104ce8d
Report errno on file opening failures and I/O errors
...
Add the underlying operating system error (usually "No such file" or
"Out of space" respectively, but highly informative when it is not)
to these error messages.
2019-07-17 09:04:02 -04:00
238b6bb3ea
Fix memory leak in mappy.aligner.map.
2019-07-08 09:50:54 -04:00
e026e18439
added the description of "SA" tag. Closes #438
2019-07-01 09:18:33 -04:00
58c2251b18
compatibility with GenBank GTP (resolves $422)
2019-06-11 09:16:03 -04:00
03dc8d5d97
test if index is built for #413
2019-06-07 09:11:11 -04:00
5cb61f8ee6
added FAQ
2019-06-06 10:47:33 -04:00
c16a1742a3
Er... Tavis doesn't have python 3.7.
2019-05-11 20:06:48 -04:00
4bd5a018c2
test python 3.7 instead of 3.6
2019-05-11 20:05:06 -04:00
05974c80f1
r943: allow long ref name for --split-index
...
Resolved #394 .
2019-05-10 15:39:41 -04:00
7bc87b4175
Release minimap2-2.17 (r941)
2019-05-04 23:49:17 -04:00
6762368cf0
r940: added the splice:hq preset
...
for high-quality CCS/mRNA splice alignment
2019-05-04 14:00:31 -04:00
c2aec88b84
r938: added --sam-hit-only; resolved #377
2019-04-30 22:40:36 -04:00
97f67a2a0a
r937: enlarge mm_mapopt_t::flag to 64 bits
2019-04-30 22:30:32 -04:00
Heng Li
mbrcic
Jun Aruga
Jared Simpson
xdudiagnoa
Torsten Seemann
John Marshall
Marcus Stoiber