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Feature with cigar #1294

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Feature with cigar #1294

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85f2f53
Add with_cigar option to get_aligned_pairs
DrYak Jun 18, 2024
643a307
Tests with_cigar in get_aligned_pair()
DrYak Jun 18, 2024
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2 changes: 1 addition & 1 deletion pysam/libcalignedsegment.pyi
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Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ class AlignedSegment:
def get_forward_sequence(self) -> Optional[str]: ...
def get_forward_qualities(self) -> Optional[array]: ...
def get_aligned_pairs(
self, matches_only: bool = ..., with_seq: bool = ...
self, matches_only: bool = ..., with_seq: bool = ..., with_cigar: bool = ...
) -> List[Tuple[int, int]]: ...
def get_blocks(self) -> List[Tuple[int, int]]: ...
def get_overlap(self, start: int, end: int) -> Optional[int]: ...
Expand Down
45 changes: 40 additions & 5 deletions pysam/libcalignedsegment.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -1973,7 +1973,7 @@ cdef class AlignedSegment:
return self.query_qualities


def get_aligned_pairs(self, matches_only=False, with_seq=False):
def get_aligned_pairs(self, matches_only=False, with_seq=False, with_cigar=False):
"""a list of aligned read (query) and reference positions.

Each item in the returned list is a tuple consisting of
Expand All @@ -1997,6 +1997,10 @@ cdef class AlignedSegment:
reference sequence. For CIGAR 'P' (padding in the reference)
operations, the third tuple element will be None. Substitutions
are lower-case. This option requires an MD tag to be present.
with_cigar : bool
If True, return an extra element in the tuple containing the
CIGAR operator (without lenght) that each particular position
tuple corresponds to.

Returns
-------
Expand All @@ -2010,6 +2014,7 @@ cdef class AlignedSegment:
cdef bam1_t * src = self._delegate
cdef bint _matches_only = bool(matches_only)
cdef bint _with_seq = bool(with_seq)
cdef bint _with_cigar = bool(with_cigar)

# TODO: this method performs no checking and assumes that
# read sequence, cigar and MD tag are consistent.
Expand All @@ -2034,11 +2039,20 @@ cdef class AlignedSegment:
l = cigar_p[k] >> BAM_CIGAR_SHIFT

if op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF:
if _with_seq:
if _with_seq and _with_cigar:
for i from pos <= i < pos + l:
result.append((qpos, i, ref_seq[r_idx], op))
r_idx += 1
qpos += 1
elif _with_seq:
for i from pos <= i < pos + l:
result.append((qpos, i, ref_seq[r_idx]))
r_idx += 1
qpos += 1
elif _with_cigar:
for i from pos <= i < pos + l:
result.append((qpos, i, op))
qpos += 1
else:
for i from pos <= i < pos + l:
result.append((qpos, i))
Expand All @@ -2047,10 +2061,18 @@ cdef class AlignedSegment:

elif op == BAM_CINS or op == BAM_CSOFT_CLIP or op == BAM_CPAD:
if not _matches_only:
if _with_seq:
if _with_seq and _with_cigar:
for i from pos <= i < pos + l:
result.append((qpos, None, None, op))
qpos += 1
elif _with_seq:
for i from pos <= i < pos + l:
result.append((qpos, None, None))
qpos += 1
elif _with_cigar:
for i from pos <= i < pos + l:
result.append((qpos, None, op))
qpos += 1
else:
for i from pos <= i < pos + l:
result.append((qpos, None))
Expand All @@ -2060,10 +2082,17 @@ cdef class AlignedSegment:

elif op == BAM_CDEL:
if not _matches_only:
if _with_seq:
if _with_seq and _with_cigar:
for i from pos <= i < pos + l:
result.append((None, i, ref_seq[r_idx], op))
r_idx += 1
elif _with_seq:
for i from pos <= i < pos + l:
result.append((None, i, ref_seq[r_idx]))
r_idx += 1
elif _with_cigar:
for i from pos <= i < pos + l:
result.append((None, i, op))
else:
for i from pos <= i < pos + l:
result.append((None, i))
Expand All @@ -2076,9 +2105,15 @@ cdef class AlignedSegment:

elif op == BAM_CREF_SKIP:
if not _matches_only:
if _with_seq:
if _with_seq and _with_cigar:
for i from pos <= i < pos + l:
result.append((None, i, None, op))
elif _with_seq:
for i from pos <= i < pos + l:
result.append((None, i, None))
elif _with_cigar:
for i from pos <= i < pos + l:
result.append((None, i, op))
else:
for i from pos <= i < pos + l:
result.append((None, i))
Expand Down
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