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
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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
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r832: fixed outdated -L. Resolved #231 and #233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
9a567e4b37
allow mappy to change scoring
2018-08-06 09:52:13 -04:00
8e606bcc06
added a `-C5` example to Getting Started
2018-08-06 09:08:33 -04:00
a1b7219b5d
explain added parameters
2018-08-05 21:32:05 -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
b32296e18f
r821: fixed memory when -y is used
2018-07-31 15:14:37 -04:00
99ecdf7b5d
mappy to support arm64 ( #203 )
2018-07-24 23:53:02 -04:00
ff9917a1c4
r819: mappy to support cs/MD
2018-07-24 23:29:55 -04:00
8c064a5f29
Fixed mm_idx_is_idx to return the correct result on Windows.
2018-07-17 09:16:33 -04:00
0e137670fc
Merge branch 'split'
2018-07-15 22:24:15 -04:00
395c8d678a
r815: fixed a memory leak
2018-07-15 22:11:32 -04:00
830da7fa27
r814: resumed versioning
2018-07-15 11:48:14 -04:00
a655cbef86
print SAM header; remove tmp files
2018-07-15 11:03:18 -04:00
4b707aac92
working with toy examples
2018-07-15 10:55:00 -04:00
951c0d1d35
apparently mm_append_cigar() wastes some memory
2018-07-14 23:47:44 -04:00
3545e35a42
pairing in the split-idx mode
2018-07-14 23:43:34 -04:00
f3417da838
bugfix: unmapped records are duplicated in output
2018-07-14 22:54:05 -04:00
e5277dbf5c
code backup
2018-07-14 22:52:36 -04:00
1a55227d5a
write hits to tmp files (unfinished)
2018-07-14 12:15:10 -04:00
5cfa621b2d
use unmapped records
2018-07-07 12:49:15 -05:00
a609a07f8c
optionally output unmapped query in PAF
2018-07-07 10:26:08 -05:00
bcf92b3c46
compute query coverage
2018-07-06 21:52:01 -05:00
097378ab90
reworked break point counting
2018-07-06 09:46:26 -04:00
10bbbe28c5
added asmstat
2018-07-05 13:22:32 -04:00
c92a6866f3
Release the GIL to allow native Python threading.
2018-07-05 08:00:27 -04:00
6908dc59a5
--splice implied when searching for splicing sites on single strand
2018-07-05 07:41:26 -04:00
50dae10421
paftools call to show statistics on longer indels
2018-07-03 14:28:09 -04:00
0517972d02
Release minimap2-2.11 (r797)
2018-06-21 00:04:08 -04:00
d46e68e6ad
r796: don't use ssize_t
2018-06-20 12:45:27 -04:00
2584a4149a
r295: use -r2000 for ava-ont, NOT for ava-pb
2018-06-20 12:24:43 -04:00
Heng Li
Torsten Seemann
Chris Rands
Mark Bicknell
Hyeshik Chang
Maël Kerbiriou