def set_pair_info(r1: AlignedSegment,
r2: AlignedSegment,
proper_pair: bool = True) -> None:
"""Resets mate pair information between reads in a pair. Requires that both r1
and r2 are mapped. Can be handed reads that already have pairing flags setup or
independent R1 and R2 records that are currently flagged as SE reads.
Args:
r1: read 1
r2: read 2 with the same queryname as r1
"""
assert not r1.is_unmapped, f"Cannot process unmapped mate {r1.query_name}/1"
assert not r2.is_unmapped, f"Cannot process unmapped mate {r2.query_name}/2"
assert r1.query_name == r2.query_name, f"Attempting to pair reads with different qnames."
for r in [r1, r2]:
r.is_paired = True
r.is_proper_pair = proper_pair
r1.is_read1 = True
r1.is_read2 = False
r2.is_read2 = True
r2.is_read1 = False
for src, dest in [(r1, r2), (r2, r1)]:
dest.next_reference_id = src.reference_id
dest.next_reference_start = src.reference_start
dest.mate_is_reverse = src.is_reverse
dest.mate_is_unmapped = False
dest.set_tag("MC", src.cigarstring)
insert_size = isize(r1, r2)
r1.template_length = insert_size
r2.template_length = -insert_size
def _set_flags(self, rec: pysam.AlignedSegment, is_r1: bool,
strand: str) -> None:
"""Appropriately sets most flag fields on the given read.
Args:
rec: the read to set the flags on
is_r1: True if the read is a R1, False if it is an R2
strand: Either "+" or "-" to indicate strand of the read
"""
rec.is_paired = True
rec.is_read1 = is_r1
rec.is_read2 = not is_r1
rec.is_qcfail = False
rec.is_duplicate = False
rec.is_secondary = False
rec.is_supplementary = False
if not rec.is_unmapped:
rec.is_reverse = strand != "+"
