skills/pysam/scripts/variant_summary.py

• positive_int · function · L21-L25 — def positive_int(value: str) -> int
• nonnegative_int · function · L28-L32 — def nonnegative_int(value: str) -> int
• build_parser · function · L35-L78 — def build_parser() -> argparse.ArgumentParser
• require_local_file · function · L81-L87 — def require_local_file(path: Path, label: str) -> Path
• variant_records · function · L90-L96 — def variant_records( variants: pysam.VariantFile, region: Optional[str], ) -> Iterator[pysam.VariantRecord]
• is_symbolic_or_breakend · function · L99-L105 — def is_symbolic_or_breakend(allele: str) -> bool
• classify_record · function · L108-L120 — def classify_record(record: pysam.VariantRecord) -> str
• filter_status · function · L123-L129 — def filter_status(record: pysam.VariantRecord) -> str
• update_substitution_counts · function · L132-L148 — def update_substitution_counts( record: pysam.VariantRecord, counts: Counter[str], ) -> None
• update_genotype_counts · function · L151-L186 — def update_genotype_counts( record: pysam.VariantRecord, counts: Counter[str], ploidy_counts: Counter[int], ) -> None
• summarize_variants · function · L189-L314 — def summarize_variants(args: argparse.Namespace) -> dict[str, Any]
• write_report · function · L317-L330 — def write_report(report: dict[str, Any], output: Optional[Path]) -> None
• main · function · L333-L358 — def main(argv: Optional[list[str]] = None) -> int