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 != "+"
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
