f4c844b143
fixed a few simple bugs and leaks
2019-04-28 16:47:12 -04:00
6420acca6d
BED I/O
2019-04-28 16:47:12 -04:00
6b391e3373
Release minimap2-2.16 (r922)
2019-02-28 15:49:24 -05:00
55e39c2d30
r921: output unmapped reads in full PAF
2019-02-27 15:03:19 -05:00
90b7b83ec7
fix typo in command line help
2019-02-27 14:46:57 -05:00
d431dc0181
r917: added --max-chain-iter to avoid worst case
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Resolves #324
2019-02-27 14:41:01 -05:00
ea84fc0a53
r917: fixed a bug in command-line parsing
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Resolves #344
2019-02-27 11:22:58 -05:00
e02bebd96d
r915: fixed a bug caused by the latest change
2019-02-14 10:04:04 -05:00
32ab6ce15b
r914: fixed two harmless division by 0
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Resolves #326
2019-02-12 19:30:49 -05:00
1739a260fb
r913: output tag "rl", length of unseedable regs
2019-02-05 14:19:17 -05:00
8b05880f73
r911: option -o to output to file ( #319 )
2019-01-29 10:42:20 -05:00
eba237f39d
r910: meaningful error message ( #320 )
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when minimap2 fails to create temporary files
2019-01-29 10:29:27 -05:00
597212b9f3
r908: added an assertion to detect a potential bug
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as in #311
2019-01-23 11:18:50 -05:00
48e230f40d
r906: de tag is wrongly calculated given "N"
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Resolves #309
2019-01-11 19:39:09 -05:00
c404f49569
Release minimap2-2.15 (r905)
2019-01-10 12:34:45 -05:00
cf2bae6e9b
r904: fixed a corner-case segfault. Resolves #307 .
2019-01-10 09:57:05 -05:00
ea2b1c5b2a
r894: added --max-qlen to filter out long query
2018-12-12 12:27:32 -05:00
2c52364527
r892: avoid de:f:0.0000
2018-11-24 21:54:28 -05:00
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
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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
91f548b497
r886: fixed two minor typos
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Resolves #264
Resolves #265
2018-11-08 12:04:14 -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
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
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resolves #252
resolves #255
2018-11-05 10:02:44 -05:00
24df95e4b8
r874: don't call x86_simd() so often
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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
42baf287a4
r866: fixed a typo; resolves #262
2018-10-30 09:11:55 -04:00
9ed56b4a25
r860: MD/cs not working with --eqx
2018-10-26 23:23:53 -04:00
377c7099a8
r858: fixed a bug; resolves #254
2018-10-22 22:47:11 -04:00
7b0a49732e
r856: wrongly reported for an unrecognized option
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Resolved #250
2018-10-19 20:07:14 -04:00
d04ac068fd
r852: a minor when large --end-bonus is in use
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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
c63a33904f
r836: fixed an integer overflow
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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
7d80d6de4a
r832: fixed outdated -L. Resolved #231 and #233
2018-09-14 22:21:33 -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
b0f39a1a61
r823: mappy to index a single sequence
2018-08-05 20:57:05 -04:00
5ab6538757
r822: added option --no-end-flt
2018-08-05 19:42:12 -04:00
Heng Li
Kevin Chan