eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -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
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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
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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
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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
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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
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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
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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
189555503a
potentially fix issue #372
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Needs someone to confirm
2019-04-30 21:49:51 -04:00
69af86657e
r935: fixed a cigar like 5I6D7I; resolved #392
2019-04-30 21:35:24 -04:00
49c6d83a8e
r934: --junc-bed to read BED12
2019-04-28 20:12:28 -04:00
f64e426a5a
r933: resume versioning
2019-04-28 17:05:37 -04:00
2bb8cbbeef
updated manpage
2019-04-28 17:02:49 -04:00
e80759c97a
--junc-bed apparently working
...
Also fixed an issue with splice alignment in the reverse strand, though this
should have a very minor effect in practice.
2019-04-28 16:47:12 -04:00
f4c844b143
fixed a few simple bugs and leaks
2019-04-28 16:47:12 -04:00
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
cdc730d573
gff2bed to output junction BED
2019-04-28 16:47:12 -04:00
6420acca6d
BED I/O
2019-04-28 16:47:12 -04:00
371bc9513a
SAM TLEN should be 0 when either read is unmapped
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this_rid/this_pos will be copied from r_prev(=r_next)'s values when this
read is unmapped (i.e., r is NULL). In this case, we can write RNEXT as
'=' but should not calculate TLEN from these placeholder values.
Similarly when the mate is unmapped (i.e., r_next is NULL).
Fixes #365 .
2019-04-05 09:36:46 -04:00
169216bfff
manpage was wrongly marked as "dirty"
2019-02-28 15:58:12 -05:00
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
ccf1680aaf
make it explicit that -x is preferred for prebuilt
2019-02-27 12:43:33 -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
19208fb06b
r916: support long cs in sam-to-paf conversion
2019-02-17 09:35:23 -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
aaf3233818
added mappy.Aligner.seq_names to return seq names
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Resolves #312
2019-01-29 12:53:20 -05:00
Heng Li
xdudiagnoa
Torsten Seemann
John Marshall
Marcus Stoiber
Kevin Chan