def set_qc_fail(rec: pysam.AlignedSegment, tool: Callable[..., Any],
reason: str) -> None:
"""Sets the QC fail flag, and adds tags containing the tool name and reason for failing.
Args:
rec: the record to fail
tool: the tool (as a callable) that failed this record
reason: the reason for failing
"""
assert '\t' not in reason, f"Reason may not contain tabs: {reason}"
rec.is_qcfail = True
rec.set_tag(QcFailToolTag, tool.__name__)
rec.set_tag(QcFailReasonTag, reason)
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 != "+"