def _make_read_unmapped(rec: AlignedSegment) -> None:
"""Removes mapping information from a read."""
if rec.is_reverse:
quals = rec.query_qualities
quals.reverse()
rec.query_sequence = dnautils.reverse_complement(rec.query_sequence)
rec.query_qualities = quals
rec.is_reverse = False
rec.reference_id = sam.NO_REF_INDEX
rec.reference_start = sam.NO_REF_POS
rec.cigar = None
rec.mapping_quality = 0
rec.template_length = 0
rec.is_duplicate = False
rec.is_secondary = False
rec.is_supplementary = False
rec.is_proper_pair = False
rec.is_unmapped = True
def _set_mate_info(self, r1: pysam.AlignedSegment,
r2: pysam.AlignedSegment) -> None:
"""Sets the mate information on a pair of sam records.
Handles cases where both reads are mapped, one of the two reads is unmapped or both reads
are unmapped.
Args:
r1: the first read in the pair
r2: the sceond read in the pair
"""
for rec in r1, r2:
rec.template_length = 0
rec.is_proper_pair = False
if r1.is_unmapped and r2.is_unmapped:
# If they're both unmapped just clean the records up
for rec, other in [(r1, r2), (r2, r1)]:
rec.reference_id = sam.NO_REF_INDEX
rec.next_reference_id = sam.NO_REF_INDEX
rec.reference_start = sam.NO_REF_POS
rec.next_reference_start = sam.NO_REF_POS
rec.is_unmapped = True
rec.mate_is_unmapped = True
rec.is_proper_pair = False
rec.mate_is_reverse = other.is_reverse
elif r1.is_unmapped or r2.is_unmapped:
# If only one is mapped/unmapped copy over the relevant stuff
(m, u) = (r1, r2) if r2.is_unmapped else (r2, r1)
u.reference_id = m.reference_id
u.reference_start = m.reference_start
u.next_reference_id = m.reference_id
u.next_reference_start = m.reference_start
u.mate_is_reverse = m.is_reverse
u.mate_is_unmapped = False
u.set_tag("MC", m.cigarstring)
m.next_reference_id = u.reference_id
m.next_reference_start = u.reference_start
m.mate_is_reverse = u.is_reverse
m.mate_is_unmapped = True
else:
# Else they are both mapped
for rec, other in [(r1, r2), (r2, r1)]:
rec.next_reference_id = other.reference_id
rec.next_reference_start = other.reference_start
rec.mate_is_reverse = other.is_reverse
rec.mate_is_unmapped = False
rec.set_tag("MC", other.cigarstring)
if r1.reference_id == r2.reference_id:
r1p = r1.reference_end if r1.is_reverse else r1.reference_start
r2p = r2.reference_end if r2.is_reverse else r2.reference_start
r1.template_length = r2p - r1p
r2.template_length = r1p - r2p
# Arbitrarily set proper pair if the we have an FR pair with isize <= 1000
if r1.is_reverse != r2.is_reverse and abs(
r1.template_length) <= 1000:
fpos, rpos = (r2p, r1p) if r1.is_reverse else (r1p, r2p)
if fpos < rpos:
r1.is_proper_pair = True
r2.is_proper_pair = True