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
66674afd09
r794: fixed a bug in seed filtering
2018-06-20 10:26:29 -04:00
e9ca0c9dab
added __version__; resolved #165
...
Not sure if this is the right way. Apparently working.
2018-06-19 15:40:26 -04:00
7e6e8ca73f
r792: fixed -Wextra warnings and resolved #184
2018-06-19 15:26:58 -04:00
408e098859
fix deserialization of zero-length reference names
2018-06-19 14:46:05 -04:00
57f37551f8
expose mm_idx_is_idx, mm_idx_load and mm_idx_dump
2018-06-19 14:46:05 -04:00
4c66b689c3
fix serialization of empty names in mm_idx_dump
2018-06-19 14:46:05 -04:00
1bde2cf076
Allow setting max_frag_len on a per alignment level
2018-06-19 14:39:30 -04:00
31fc0f218a
Allow setting max_frag_len parameter in Aligner class
2018-06-19 14:39:30 -04:00
3d3bcc29a8
Fix CIGAR reallocation with --eqx
...
Fix the logic that calculates the number of CIGAR entries when
match "M" entries are expanded into "=" and "X". The number
of entries depends not on the number of mismatches but rather
on the number of transitions between "=" to "X".
2018-06-19 14:37:41 -04:00
99dcd75f64
added support for 64 bit ARM architectures
2018-06-19 14:28:45 -04:00
154d2caf5b
r784: support the =/X CIGAR operators ( #156 )
2018-05-30 16:11:22 -04:00
a3afeec0b2
r783: reverted to r781 ( #155 )
2018-05-30 15:25:34 -04:00
3573784b4d
r782: no mask a chain having long ref ovlp ( #155 )
2018-05-30 13:53:45 -04:00
872f300955
r781: fixed the buggy heapmerge ( resolves #166 )
2018-05-30 11:55:14 -04:00
d7b61a039e
updated citation
2018-05-30 11:11:55 -04:00
248158a3e1
Resolved #168 : citing the manpage for cs
2018-05-30 11:03:16 -04:00
9f4309c376
r777: avoid skipping too many seeds
2018-05-11 10:25:18 -04:00
463f9309f9
Merge branch 'hot-fix' into fix-long-gap
2018-05-11 10:13:19 -04:00
abe989e355
the previous fix on int overflow is incomplete
2018-05-11 10:12:57 -04:00
881b4ca3a2
r774: Merge branch 'hot-fix' into fix-long-gap
2018-05-11 10:02:17 -04:00
10c6dd2551
r773: fixed an integer overflow
2018-05-11 10:01:23 -04:00
7ec6721c44
r772: option -Y not working
2018-05-11 10:00:11 -04:00
e61812ee55
reduced gap len to trigger bad seed filtering
2018-05-01 16:17:21 -04:00
734ac379bb
r770: matching N bases not working properly ( #155 )
2018-04-30 19:55:23 -04:00
Heng Li
Mark Bicknell
Hyeshik Chang
Maël Kerbiriou
Ilya Kolpakov
mvdbeek
Aaron Wenger
Hasindu Gamaarachchi