← Về thư mục
skills/pysam/scripts/inspect_hts.py
- positive_int · function · L23-L27 — def positive_int(value: str) -> int
- nonnegative_int · function · L30-L34 — def nonnegative_int(value: str) -> int
- detect_kind · function · L37-L84 — def detect_kind(path: Path) -> str
- build_parser · function · L87-L131 — def build_parser() -> argparse.ArgumentParser
- require_local_file · function · L134-L140 — def require_local_file(path: Path, label: str) -> Path
- limited · function · L143-L146 — def limited(values: list[Any], maximum: int) -> tuple[list[Any], bool]
- contig_records · function · L149-L158 — def contig_records( names: tuple[str, ...] | list[str], lengths: tuple[int, ...] | list[int], maximum: int, ) -> tuple[list[dict[str, Any]], bool]
- alignment_mode · function · L161-L167 — def alignment_mode(path: Path) -> str
- inspect_alignment · function · L170-L249 — def inspect_alignment( path: Path, *, reference: Optional[Path], index: Optional[Path], threads: int, max_items: int, include_identifiers: bool, ) -> dict[str, Any]
- variant_index_loaded · function · L252-L256 — def variant_index_loaded(variants: pysam.VariantFile) -> bool
- inspect_variant · function · L259-L311 — def inspect_variant( path: Path, *, index: Optional[Path], threads: int, max_items: int, include_identifiers: bool, ) -> dict[str, Any]
- inspect_fasta · function · L314-L337 — def inspect_fasta( path: Path, *, index: Optional[Path], max_items: int, ) -> dict[str, Any]
- inspect_fastx · function · L340-L350 — def inspect_fastx(path: Path) -> dict[str, Any]
- inspect_tabix · function · L353-L376 — def inspect_tabix( path: Path, *, index: Optional[Path], threads: int, max_items: int, ) -> dict[str, Any]
- inspect_file · function · L379-L437 — def inspect_file(args: argparse.Namespace) -> dict[str, Any]
- write_report · function · L440-L453 — def write_report(report: dict[str, Any], output: Optional[Path]) -> None
- main · function · L456-L481 — def main(argv: Optional[list[str]] = None) -> int