main module

hairpin2(records: Iterable[VariantRecord], sample_to_alignment: Mapping[str, AlignmentFile], configd: dict[str, Any], quiet: int = 0) → Generator[VariantRecord, Any, Any]

read-aware artefactual variant flagging algorithms.

Flag variants in VCF using statistics calculated from supporting reads found in ALIGNMENTS and emit the flagged VCF to stdout.

NOTE: requires VariantFileHeader associated with variant records to have been initialised correctly for the output