skills/pysam/scripts/alignment_qc.py

• positive_int · function · L20-L24 — def positive_int(value: str) -> int
• nonnegative_int · function · L27-L31 — def nonnegative_int(value: str) -> int
• build_parser · function · L34-L71 — def build_parser() -> argparse.ArgumentParser
• require_local_file · function · L74-L80 — def require_local_file(path: Path, label: str) -> Path
• alignment_mode · function · L83-L91 — def alignment_mode(path: Path) -> str
• ratio · function · L94-L95 — def ratio(numerator: int, denominator: int) -> Optional[float]
• average · function · L98-L99 — def average(total: int, count: int) -> Optional[float]
• selected_reads · function · L102-L108 — def selected_reads( alignments: pysam.AlignmentFile, region: Optional[str], ) -> Iterator[pysam.AlignedSegment]
• empty_counts · function · L111-L130 — def empty_counts() -> dict[str, int]
• inspect_alignments · function · L133-L278 — def inspect_alignments(args: argparse.Namespace) -> dict[str, Any]
• write_report · function · L281-L294 — def write_report(report: dict[str, Any], output: Optional[Path]) -> None
• main · function · L297-L322 — def main(argv: Optional[list[str]] = None) -> int