128476efc9
r891: compute gap-compressed divergence
2018-11-24 21:50:49 -05:00
1b3a6a0fe5
r890: removed "register" ( #261 )
2018-11-19 13:57:31 -05:00
83a8ee7038
r888: fixed incorrect CIGAR when --eqx in use
...
This was caused by mm_fix_cigar() which may change query/target offset in very
rare cases. Generating EQX has to beware of this change.
Resolves #266
2018-11-18 14:22:29 -05:00
62bbadf668
r887: fixed a bug in asmgene
2018-11-11 21:35:19 -05:00
91f548b497
r886: fixed two minor typos
...
Resolves #264
Resolves #265
2018-11-08 12:04:14 -05:00
cdaf46665a
r885: compute dup with asmstat
2018-11-07 00:26:05 -05:00
6596c63dcd
r884: for C++ compatibility ( #261 )
2018-11-06 22:07:11 -05:00
59f23f7579
Release minimap2-2.14 (r883)
2018-11-06 00:03:16 -05:00
5e55e397e9
r882: guard against -E0 ( #263 )
2018-11-05 23:36:12 -05:00
88c421e8de
r881: a recent change reduces sr accuracy
2018-11-05 22:03:59 -05:00
3db5bfe6e5
r880: fixed false wrong FASTA/Q alert
2018-11-05 20:52:07 -05:00
83dfdd5f50
draft release note
2018-11-05 20:07:57 -05:00
8a2b1cd4c9
updated mappy for extra option max_sw_mat
2018-11-05 19:28:44 -05:00
1ede8ca170
r877: renamed cap-sw-mat to cap-sw-mem
2018-11-05 11:46:38 -05:00
13981404e2
r876: skip DP if taking too much RAM ( #259 )
2018-11-05 11:43:10 -05:00
fd64dd26f6
r875: warn given incorrect FASTA/Q
...
resolves #252
resolves #255
2018-11-05 10:02:44 -05:00
24df95e4b8
r874: don't call x86_simd() so often
...
This takes a few percent of time in profiler.
2018-11-05 09:20:35 -05:00
a8ee48c2ce
r873: comforming to C99/C11; resolves #261
2018-11-05 08:25:07 -05:00
09e089c3dc
r872: choose the longest isoform
2018-11-04 23:48:50 -05:00
e46cbb7d84
r871: print erroneous genes
2018-11-04 20:37:06 -05:00
57ec73ec6c
r870: separate <50% and <10%
2018-11-04 19:31:25 -05:00
9e27575387
r869: classify incomplete genes
2018-11-04 19:21:55 -05:00
b4ad8d8bf0
added asmgene
...
improvements coming; not made public yet
2018-11-04 17:24:05 -05:00
e315b9fada
hidden options to control bp calculation
2018-11-04 16:36:04 -05:00
42baf287a4
r866: fixed a typo; resolves #262
2018-10-30 09:11:55 -04:00
2ceba22a7a
fixed a typo in manpage
2018-10-28 11:51:02 -04:00
9ed56b4a25
r860: MD/cs not working with --eqx
2018-10-26 23:23:53 -04:00
ecb6c5c36c
Document --no-pairing ( #256 )
2018-10-23 10:00:21 -04:00
377c7099a8
r858: fixed a bug; resolves #254
2018-10-22 22:47:11 -04:00
51e2abfa60
clarify that minimap2 may miss small exons
2018-10-22 11:16:16 -04:00
7b0a49732e
r856: wrongly reported for an unrecognized option
...
Resolved #250
2018-10-19 20:07:14 -04:00
20268a6068
updated the copyright holder
2018-10-18 11:11:17 -04:00
d04ac068fd
r852: a minor when large --end-bonus is in use
...
We may use a large --end-bonus to mimic end-to-end alignment. In the short-read
mode, the candidate alignment region may be out of the band, which leads to
truncated alignment.
2018-10-15 21:28:27 -04:00
5d5d392c02
Release minimap2-2.13 (r850)
2018-10-11 13:18:31 -04:00
170863e553
r849: option -P doesn't work
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I don't know why I haven't found it at the beginning.
2018-10-04 16:11:59 -04:00
97f97306a4
r847: guard against -N0
2018-09-27 15:13:44 -04:00
1077b7ddc8
r846: added --hard-mask-level for #244
2018-09-27 14:46:26 -04:00
c57b59f02f
r845: log peak memory
2018-09-23 20:27:49 -04:00
34be359e25
Add -s sample option for VCF output
2018-09-19 18:24:47 -04:00
8b12da8b0f
removed a useless dependency (not in repo)
2018-09-17 13:59:25 -04:00
c63a33904f
r836: fixed an integer overflow
...
Forgot this one.
2018-09-14 23:29:31 -04:00
70b0fede64
r835: improved help message. Resolved #232
2018-09-14 22:29:25 -04:00
0b681e51e7
Merge remote-tracking branch 'remotes/origin/master'
2018-09-14 22:22:20 -04:00
7d80d6de4a
r832: fixed outdated -L. Resolved #231 and #233
2018-09-14 22:21:33 -04:00
791e89ce0f
PEP8 and other minor styles changes
2018-09-12 10:58:56 -04:00
98c48a1c45
Fixed wrong version links in the cookbook
2018-09-03 09:07:34 -04:00
63d397120a
removed getopt.c from MANIFEST
2018-09-01 21:30:46 -04:00
7998fe9906
r829: replaced musl's getopt with ketopt
2018-09-01 21:18:02 -04:00
3a119d606f
r828: --MD to support spliced alignment
2018-08-22 10:47:45 -04:00
a5eafb75f9
Release minimap2-2.12 (r827)
2018-08-06 12:44:39 -04:00
Heng Li
Torsten Seemann
Chris Rands