c3d461e22a
mappy check index flags before mapping
...
mappy creates a CIGAR string by default (`-c` flag) and so is
incompatible with indexes that are created using the `--idx-no-seq`
flag.
The previous implementation of mappy did not check for the `MM_I_NO_SEQ`
flag and would seg fault when attempting to map a read or retrieve a
reference sequence from the index. This patch adds a check to both
`mappy.Aligner.seq` and `mappy.Aligner.map` and returns `None` if there
is no index sequences. I've chose `None` as this is inline with the
behaviour of mappy for reads that do not align/retreiving sequences that
aren't in the index, however it might be better to raise an exception so
that this error is distinct and can be communicated to the caller.
2023-04-19 21:49:58 -04:00
fe35e679e9
Release minimap2-2.24 (r1122)
2021-12-26 15:14:54 -05:00
d0cff3eb36
Release minimap2-2.23 (r1111)
2021-11-18 17:11:48 -05:00
7358a1ead1
Release minimap2-2.22 (r1101)
2021-08-07 11:30:31 -04:00
581f2d7123
Release minimap2-2.21 (r1071)
2021-07-06 13:18:55 -04:00
177eef259d
Use the full MIDNSHP=X string whenever printing CIGAR strings
...
Define MM_CIGAR_STR to the full string of CIGAR operators (including
the 'B' operator as well) and use it throughout the C code.
It would be possible to use it from the Cython code too, but it's easier
to keep that as a Cython string literal to avoid adding extra runtime
code to handle locale conversion.
2021-07-02 13:03:03 -04:00
15471bd629
Release minimap2-2.20 (r1061)
2021-05-27 15:26:04 -04:00
ef09ccf104
Release minimap2-2.19 (r1055)
2021-05-26 21:01:03 -04:00
b6ff332de1
Release minimap2-2.18 (r1015)
2021-04-09 13:33:34 -04:00
238b6bb3ea
Fix memory leak in mappy.aligner.map.
2019-07-08 09:50:54 -04:00
03dc8d5d97
test if index is built for #413
2019-06-07 09:11:11 -04:00
7bc87b4175
Release minimap2-2.17 (r941)
2019-05-04 23:49:17 -04:00
189555503a
potentially fix issue #372
...
Needs someone to confirm
2019-04-30 21:49:51 -04:00
6b391e3373
Release minimap2-2.16 (r922)
2019-02-28 15:49:24 -05:00
aaf3233818
added mappy.Aligner.seq_names to return seq names
...
Resolves #312
2019-01-29 12:53:20 -05:00
c404f49569
Release minimap2-2.15 (r905)
2019-01-10 12:34:45 -05:00
59f23f7579
Release minimap2-2.14 (r883)
2018-11-06 00:03:16 -05:00
5d5d392c02
Release minimap2-2.13 (r850)
2018-10-11 13:18:31 -04:00
9a567e4b37
allow mappy to change scoring
2018-08-06 09:52:13 -04:00
b0f39a1a61
r823: mappy to index a single sequence
2018-08-05 20:57:05 -04:00
ff9917a1c4
r819: mappy to support cs/MD
2018-07-24 23:29:55 -04:00
0517972d02
Release minimap2-2.11 (r797)
2018-06-21 00:04:08 -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
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
24a4808826
r718: retrieve sequence from the index
2018-02-23 10:18:26 -05:00
29ed675ee5
bugfix: in-place revcomp() not working
2018-02-20 11:05:54 -05:00
7dc7097208
added reverse complement
2018-02-20 09:41:25 -05:00
090361c25b
fixed a typo in mappy ( #117 )
2018-02-16 21:10:57 -05:00
46d6349af4
r670: added PE support to mappy
...
and minor code cleanup
2018-01-31 11:33:08 -05:00
4f77b0c1ed
Fix typo in strand property
2017-11-11 01:18:44 +00:00
29a26e3eea
Bug fix with byte strings in Python3
2017-11-09 13:57:15 +00:00
b24c9c90c7
updated mappy and example.c
2017-10-16 11:15:07 -04:00
cf93e5c0a1
more functional minimap2.py; added categories
2017-09-17 17:06:39 -04:00
0b660c70e2
syntax error
2017-09-17 16:02:06 -04:00
5715c423ff
exposed timer and verbose-level to mappy
2017-09-17 15:21:36 -04:00
c8a019fae8
exposed fasta/q reader to mappy
2017-09-17 14:41:59 -04:00
d5012a1b17
this is embarrassing: rename again to mappy
2017-09-17 00:05:30 -04:00
Alex Payne
Heng Li
John Marshall
Marcus Stoiber
mvdbeek
cwright
martinghunt