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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.
This commit is contained in:
Alex Payne 2023-01-12 13:22:46 +00:00 committed by Heng Li
parent c41518ae85
commit c3d461e22a
1 changed files with 2 additions and 0 deletions
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2
python/mappy.pyx
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@ -172,6 +172,7 @@ cdef class Aligner:
cdef cmappy.mm_mapopt_t map_opt
if self._idx == NULL: return
if ((self.map_opt.flag & 4) and (self._idx.flag & 2)): return
map_opt = self.map_opt
if max_frag_len is not None: map_opt.max_frag_len = max_frag_len
if extra_flags is not None: map_opt.flag |= extra_flags
@ -217,6 +218,7 @@ cdef class Aligner:
cdef int l
cdef char *s
if self._idx == NULL: return
if ((self.map_opt.flag & 4) and (self._idx.flag & 2)): return
s = cmappy.mappy_fetch_seq(self._idx, name.encode(), start, end, &l)
if l == 0: return None
r = s[:l] if isinstance(s, str) else s[:l].decode()