skills/onekgpd/scripts/onekgpd_api.py

• _fail · function · L65-L68 — def _fail(msg: str) -> NoReturn
• _split_csv · function · L71-L73 — def _split_csv(s: str) -> list[str]
• _save_json · function · L76-L86 — def _save_json(data: Any, prefix: str, output_path: str | None = None) -> str
• _emit · function · L89-L94 — def _emit(data: Any, prefix: str, summary_lines: list[str], output: str | None) -> None
• _call_with_retry · function · L97-L110 — def _call_with_retry(fn)
• _parse_region_str · function · L118-L129 — def _parse_region_str(s: str) -> Region
• _build_regions · function · L132-L151 — def _build_regions(args) -> tuple[Region | None, list[Region] | None]
• _zygosity · function · L154-L160 — def _zygosity(args) -> tuple[bool, bool]
• _build_annotation_filter · function · L190-L218 — def _build_annotation_filter(args) -> AnnotationFilter | None
• _chr_to_str · function · L226-L228 — def _chr_to_str(chrom) -> str
• _region_one_label · function · L231-L232 — def _region_one_label(r: Region) -> str
• _region_label · function · L235-L238 — def _region_label(region: Region | None, regions: list[Region] | None) -> str
• _zyg_label · function · L241-L246 — def _zyg_label(hom: bool, het: bool) -> str
• _variant_to_dict · function · L249-L274 — def _variant_to_dict(v) -> dict
• _filters_echo · function · L277-L295 — def _filters_echo(args) -> dict
• _request_echo · function · L298-L315 — def _request_echo(args, *, samples, region, regions, hom, het) -> dict
• _run_count_variants · function · L323-L357 — def _run_count_variants(args, samples: list[str] | None) -> None
• fetch · function · L328-L339 — def fetch()
• _run_select_variants · function · L360-L435 — def _run_select_variants(args, samples: list[str] | None) -> None
• fetch · function · L367-L398 — def fetch()
• cmd_count_variants · function · L438-L439 — def cmd_count_variants(args) -> None
• cmd_count_variants_in_samples · function · L442-L443 — def cmd_count_variants_in_samples(args) -> None
• cmd_select_variants · function · L446-L447 — def cmd_select_variants(args) -> None
• cmd_select_variants_in_samples · function · L450-L451 — def cmd_select_variants_in_samples(args) -> None
• cmd_count_samples · function · L454-L487 — def cmd_count_samples(args) -> None
• fetch · function · L459-L469 — def fetch()
• cmd_select_samples · function · L490-L536 — def cmd_select_samples(args) -> None
• fetch · function · L495-L507 — def fetch()
• cmd_count_samples_hom_ref · function · L539-L565 — def cmd_count_samples_hom_ref(args) -> None
• fetch · function · L540-L542 — def fetch()
• cmd_select_samples_hom_ref · function · L568-L587 — def cmd_select_samples_hom_ref(args) -> None
• fetch · function · L569-L571 — def fetch()
• cmd_kinship · function · L590-L616 — def cmd_kinship(args) -> None
• fetch · function · L591-L593 — def fetch()
• cmd_dataset_info · function · L619-L653 — def cmd_dataset_info(args) -> None
• fetch · function · L620-L622 — def fetch()
• _add_annotation_flags · function · L661-L689 — def _add_annotation_flags(p: argparse.ArgumentParser) -> None
• build_parser · function · L692-L780 — def build_parser() -> argparse.ArgumentParser
• main · function · L783-L790 — def main(argv: list[str] | None = None) -> None: # Incompleteness is surfaced via result metadata and the summary, not warnings.