706 lines
22 KiB
Python
706 lines
22 KiB
Python
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#!/usr/bin/env python3
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"""Run Stage 09 SNP/INDEL selection from the authoritative Stage08 VCF."""
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from __future__ import annotations
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import argparse
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from datetime import datetime, timezone
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import fcntl
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import gzip
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import json
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import os
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from pathlib import Path
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import re
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import shutil
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import subprocess
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import sys
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from typing import Any
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import uuid
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from gfa_core.wgs_scientific_identity import (
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build_wgs_analysis_id,
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sha256_file,
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)
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from gfa_core.wgs_upstream_manifest import resolve_wgs_artifacts
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STAGE = "wgs_variant_select"
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ROLES = (
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"selected_snp_vcf",
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"selected_snp_vcf_index",
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"selected_indel_vcf",
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"selected_indel_vcf_index",
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"variant_select_report",
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)
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def build_parser() -> argparse.ArgumentParser:
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parser = argparse.ArgumentParser(
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description="Select SNPs and INDELs from authoritative Stage08 VCF"
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)
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parser.add_argument("--workspace", required=True)
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parser.add_argument("--job-id", required=True)
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parser.add_argument("--prefix", required=True)
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parser.add_argument("--joint-manifest", required=True)
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parser.add_argument(
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"--method", choices=("gatk", "bcftools"), default="gatk"
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)
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parser.add_argument("--gatk", default="gatk")
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parser.add_argument("--bcftools", default="bcftools")
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return parser
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def _atomic_json(path: Path, payload: dict[str, Any]) -> None:
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temporary = path.with_name(f".{path.name}.{uuid.uuid4().hex}.tmp")
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temporary.write_text(
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json.dumps(payload, ensure_ascii=False, indent=2) + "\n",
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encoding="utf-8",
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)
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os.replace(temporary, path)
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def _safe_component(value: str, label: str) -> None:
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if not re.fullmatch(r"[A-Za-z0-9][A-Za-z0-9_.-]*", value or ""):
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raise ValueError(f"{label} must be a non-empty safe path component")
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def _authority_header(
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path: str | Path,
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*,
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workspace: Path,
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prefix: str,
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job_id: str,
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) -> dict[str, Any]:
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try:
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manifest = json.loads(Path(path).read_text(encoding="utf-8"))
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except (OSError, UnicodeError, json.JSONDecodeError) as exc:
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raise ValueError(
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"wgs_joint_genotyping authority Manifest is unreadable"
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) from exc
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if (
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not isinstance(manifest, dict)
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or manifest.get("stage") != "wgs_joint_genotyping"
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or manifest.get("status") != "success"
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):
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raise ValueError(
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"wgs_joint_genotyping authority Manifest is not successful"
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)
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if (
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manifest.get("prefix") != prefix
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or manifest.get("job_id") != job_id
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or manifest.get("workspace") != str(workspace)
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):
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raise ValueError(
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"wgs_joint_genotyping authority Manifest identity mismatch"
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)
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return manifest
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def _invocation_path(command: str) -> Path:
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resolved = shutil.which(command)
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if not resolved:
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raise RuntimeError(f"executable is unavailable: {command}")
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return Path(resolved).absolute()
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def _executable_path(command: str) -> Path:
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return _invocation_path(command).resolve()
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def _environment(command: str) -> dict[str, str]:
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return {
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**os.environ,
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"PATH": str(_invocation_path(command).parent)
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+ os.pathsep
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+ os.environ.get("PATH", ""),
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}
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def _checked(
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command: list[str], label: str
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) -> subprocess.CompletedProcess[str]:
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result = subprocess.run(
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command,
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text=True,
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capture_output=True,
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check=False,
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env=_environment(command[0]),
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)
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if result.returncode:
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detail = (result.stderr or result.stdout).strip()
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raise RuntimeError(
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f"{label} failed with exit code {result.returncode}: {detail}"
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)
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return result
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def _run_logged(command: list[str], log: Any, label: str) -> None:
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log.write(f"{label} argv: {json.dumps(command)}\n")
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log.flush()
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result = subprocess.run(
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command,
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stdout=log,
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stderr=subprocess.STDOUT,
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text=True,
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check=False,
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env=_environment(command[0]),
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)
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log.write(f"{label} exit={result.returncode}\n")
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log.flush()
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if result.returncode:
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raise RuntimeError(f"{label} failed with exit code {result.returncode}")
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def _tool_version(command: str, label: str) -> str:
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result = _checked([command, "--version"], f"{label} version check")
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lines = (result.stdout or result.stderr).strip().splitlines()
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if not lines:
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raise RuntimeError(f"{label} version check produced no version")
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return lines[0]
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def _vcf_summary(
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path: Path,
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expected_kind: str | None = None,
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*,
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allow_empty: bool = False,
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) -> tuple[list[str], str, int, str]:
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if not path.is_file() or path.stat().st_size <= 0:
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raise RuntimeError("VCF is missing or empty")
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samples: list[str] | None = None
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interval = ""
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fallback_interval = ""
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region_row = ""
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records = 0
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try:
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with gzip.open(path, "rt", encoding="utf-8") as handle:
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for raw in handle:
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line = raw.rstrip("\n")
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if line.startswith("#CHROM\t"):
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fields = line.split("\t")
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if len(fields) < 10:
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raise RuntimeError("VCF has no sample columns")
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samples = fields[9:]
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elif line.startswith("##contig=<ID=") and not region_row:
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contig = line[len("##contig=<ID="):].split(",", 1)[0]
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if contig:
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fallback_interval = f"{contig}:1-1"
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region_row = f"{contig}\t1\t1\n"
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elif line and not line.startswith("#"):
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fields = line.split("\t")
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if len(fields) < 10:
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raise RuntimeError("VCF record is invalid")
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ref = fields[3]
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alts = fields[4].split(",")
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is_snp = (
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len(ref) == 1
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and bool(alts)
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and all(len(alt) == 1 for alt in alts)
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)
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is_indel = any(len(alt) != len(ref) for alt in alts)
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if expected_kind == "SNP" and not is_snp:
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raise RuntimeError("selected SNP VCF contains non-SNP")
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if expected_kind == "INDEL" and not is_indel:
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raise RuntimeError(
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"selected INDEL VCF contains non-INDEL"
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)
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try:
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position = int(fields[1])
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except ValueError as exc:
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raise RuntimeError(
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"VCF record position is invalid"
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) from exc
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if not fields[0] or position < 1:
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raise RuntimeError("VCF record position is invalid")
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if not interval:
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interval = f"{fields[0]}:{position}-{position}"
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region_row = (
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f"{fields[0]}\t{position}\t{position}\n"
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)
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records += 1
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except (OSError, UnicodeError) as exc:
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raise RuntimeError("VCF is unreadable") from exc
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if not interval and allow_empty:
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interval = fallback_interval
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if (
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samples is None
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or not samples
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or len(samples) != len(set(samples))
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or (records < 1 and not allow_empty)
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or not interval
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or not region_row
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):
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raise RuntimeError("VCF content is incomplete")
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return samples, interval, records, region_row
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def _query_index(
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bcftools: str,
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vcf: Path,
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region_row: str,
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scratch: Path,
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log: Any,
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label: str,
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) -> None:
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regions = scratch / f".{label}.{uuid.uuid4().hex}.regions.tsv"
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regions.write_text(region_row, encoding="utf-8")
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try:
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_run_logged(
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[bcftools, "view", "-H", "-R", str(regions), str(vcf)],
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log,
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f"{label} indexed query",
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)
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finally:
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regions.unlink(missing_ok=True)
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def _select_gatk(
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gatk: str,
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source: Path,
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output: Path,
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kind: str,
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log: Any,
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) -> None:
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_run_logged(
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[
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gatk,
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"SelectVariants",
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"-V",
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str(source),
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"-O",
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str(output),
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"-select-type-to-include",
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kind,
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],
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log,
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f"GATK SelectVariants {kind}",
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)
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_run_logged(
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[gatk, "IndexFeatureFile", "-I", str(output)],
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log,
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f"GATK IndexFeatureFile {kind}",
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)
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def _select_bcftools(
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bcftools: str,
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source: Path,
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output: Path,
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kind: str,
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log: Any,
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) -> None:
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variant_type = "snps" if kind == "SNP" else "indels"
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_run_logged(
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[
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bcftools,
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"view",
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"-v",
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variant_type,
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"-Oz",
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"-o",
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str(output),
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str(source),
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],
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log,
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f"bcftools select {kind}",
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)
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_run_logged(
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[bcftools, "index", "--tbi", str(output)],
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log,
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f"bcftools index {kind}",
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)
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def _postflight(
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*,
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method: str,
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gatk: str,
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bcftools: str,
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output: Path,
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index: Path,
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kind: str,
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expected_samples: list[str],
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log: Any,
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) -> int:
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if index != Path(f"{output}.tbi"):
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raise RuntimeError(f"{kind} index is not its VCF sidecar")
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if not index.is_file() or index.stat().st_size <= 0:
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raise RuntimeError(f"{kind} index is missing or empty")
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samples, interval, records, region_row = _vcf_summary(
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output, kind, allow_empty=True
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)
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if samples != expected_samples:
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raise RuntimeError(f"{kind} sample header mismatch")
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if method == "gatk":
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command = [
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gatk,
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"ValidateVariants",
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"-V",
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str(output),
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"-L",
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interval,
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]
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command.extend(
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[
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"--validation-type-to-exclude", "ALLELES",
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"--validation-type-to-exclude", "REF",
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]
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)
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_run_logged(
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command,
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log,
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f"GATK ValidateVariants {kind}",
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)
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else:
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_query_index(
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bcftools, output, region_row, output.parent, log, kind
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)
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_run_logged(
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[bcftools, "stats", str(output)],
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log,
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f"bcftools stats {kind}",
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)
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return records
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def _artifact(
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workspace: Path,
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source: Path,
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destination: Path,
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role: str,
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) -> dict[str, Any]:
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size = source.stat().st_size
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return {
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"artifact": role,
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"role": role,
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"path": str(destination.relative_to(workspace)),
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"full_path": str(destination.resolve()),
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"type": source.suffix.lstrip(".") or "file",
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"size": size,
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"size_bytes": size,
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"sha256": sha256_file(source),
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}
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def _publish(
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bundle: Path,
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destination: Path,
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manifest_work: Path,
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authority: Path,
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started_at: str,
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) -> bool:
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lock_path = authority.parent.parent / ".locks" / f"{authority.stem}.lock"
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lock_path.parent.mkdir(parents=True, exist_ok=True)
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with lock_path.open("a+", encoding="utf-8") as lock:
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|
|
fcntl.flock(lock.fileno(), fcntl.LOCK_EX)
|
||
|
|
if authority.is_file():
|
||
|
|
try:
|
||
|
|
current = json.loads(authority.read_text(encoding="utf-8"))
|
||
|
|
if (
|
||
|
|
current.get("status") == "success"
|
||
|
|
and str(current.get("start_time") or "") >= started_at
|
||
|
|
):
|
||
|
|
return False
|
||
|
|
except Exception:
|
||
|
|
pass
|
||
|
|
destination.parent.mkdir(parents=True, exist_ok=True)
|
||
|
|
os.replace(bundle, destination)
|
||
|
|
os.replace(manifest_work, authority)
|
||
|
|
return True
|
||
|
|
|
||
|
|
|
||
|
|
def _failure(
|
||
|
|
args: argparse.Namespace, run_id: str, started_at: str, error: str
|
||
|
|
) -> dict[str, Any]:
|
||
|
|
payload = {
|
||
|
|
"manifest_version": "1.0",
|
||
|
|
"stage": STAGE,
|
||
|
|
"status": "failed",
|
||
|
|
"prefix": args.prefix,
|
||
|
|
"job_id": args.job_id,
|
||
|
|
"run_id": run_id,
|
||
|
|
"start_time": started_at,
|
||
|
|
"method": args.method,
|
||
|
|
"artifacts": {},
|
||
|
|
"errors": [error],
|
||
|
|
}
|
||
|
|
if (
|
||
|
|
args.method == "gatk"
|
||
|
|
and bool(getattr(args, "_fallback_eligible", False))
|
||
|
|
):
|
||
|
|
payload["fallback_method"] = "bcftools"
|
||
|
|
return payload
|
||
|
|
|
||
|
|
|
||
|
|
def _publish_failure(
|
||
|
|
authority: Path,
|
||
|
|
args: argparse.Namespace,
|
||
|
|
run_id: str,
|
||
|
|
started_at: str,
|
||
|
|
error: str,
|
||
|
|
) -> None:
|
||
|
|
lock_path = authority.parent.parent / ".locks" / f"{authority.stem}.lock"
|
||
|
|
lock_path.parent.mkdir(parents=True, exist_ok=True)
|
||
|
|
with lock_path.open("a+", encoding="utf-8") as lock:
|
||
|
|
fcntl.flock(lock.fileno(), fcntl.LOCK_EX)
|
||
|
|
failure_path = (
|
||
|
|
authority
|
||
|
|
if not authority.exists()
|
||
|
|
else authority.parent
|
||
|
|
/ (
|
||
|
|
f"{args.prefix}.{STAGE}.{args.method}.failed."
|
||
|
|
f"{run_id}.manifest.json"
|
||
|
|
)
|
||
|
|
)
|
||
|
|
_atomic_json(
|
||
|
|
failure_path, _failure(args, run_id, started_at, error)
|
||
|
|
)
|
||
|
|
|
||
|
|
|
||
|
|
def run(args: argparse.Namespace) -> int:
|
||
|
|
args._fallback_eligible = False
|
||
|
|
workspace = Path(args.workspace).resolve()
|
||
|
|
run_id = uuid.uuid4().hex
|
||
|
|
started_at = datetime.now(timezone.utc).isoformat()
|
||
|
|
final = workspace / "final"
|
||
|
|
final.mkdir(parents=True, exist_ok=True)
|
||
|
|
try:
|
||
|
|
_safe_component(args.prefix, "prefix")
|
||
|
|
except ValueError as exc:
|
||
|
|
_atomic_json(
|
||
|
|
final / f"{STAGE}.{args.method}.failed.{run_id}.manifest.json",
|
||
|
|
_failure(args, run_id, started_at, str(exc)),
|
||
|
|
)
|
||
|
|
print(f"{STAGE} failed: {exc}", file=sys.stderr)
|
||
|
|
return 1
|
||
|
|
authority = (
|
||
|
|
final / f"{args.prefix}.{STAGE}.{args.method}.manifest.json"
|
||
|
|
)
|
||
|
|
try:
|
||
|
|
header = _authority_header(
|
||
|
|
args.joint_manifest,
|
||
|
|
workspace=workspace,
|
||
|
|
prefix=args.prefix,
|
||
|
|
job_id=args.job_id,
|
||
|
|
)
|
||
|
|
sample_set_id = str(header.get("wgs_sample_set_id") or "")
|
||
|
|
reference_id = str(header.get("wgs_reference_id") or "")
|
||
|
|
upstream_analysis_id = str(header.get("wgs_analysis_id") or "")
|
||
|
|
if not sample_set_id or not reference_id or not upstream_analysis_id:
|
||
|
|
raise ValueError(
|
||
|
|
"wgs_joint_genotyping scientific lineage is incomplete"
|
||
|
|
)
|
||
|
|
resolved = resolve_wgs_artifacts(
|
||
|
|
args.joint_manifest,
|
||
|
|
"wgs_joint_genotyping",
|
||
|
|
("joint_vcf", "joint_vcf_index"),
|
||
|
|
sample_set_id,
|
||
|
|
reference_id,
|
||
|
|
upstream_analysis_id,
|
||
|
|
)
|
||
|
|
if any(len(resolved[role]) != 1 for role in resolved):
|
||
|
|
raise RuntimeError(
|
||
|
|
"authoritative joint VCF and TBI must be singletons"
|
||
|
|
)
|
||
|
|
joint_vcf = resolved["joint_vcf"][0].path
|
||
|
|
joint_index = resolved["joint_vcf_index"][0].path
|
||
|
|
if joint_index != Path(f"{joint_vcf}.tbi"):
|
||
|
|
raise RuntimeError("joint VCF index is not its declared sidecar")
|
||
|
|
expected_samples = (header.get("metrics") or {}).get(
|
||
|
|
"output_sample_ids"
|
||
|
|
)
|
||
|
|
if (
|
||
|
|
not isinstance(expected_samples, list)
|
||
|
|
or not expected_samples
|
||
|
|
or expected_samples != sorted(set(expected_samples))
|
||
|
|
or (header.get("metrics") or {}).get("input_sample_ids")
|
||
|
|
!= expected_samples
|
||
|
|
):
|
||
|
|
raise RuntimeError("joint VCF sample set is incomplete")
|
||
|
|
(
|
||
|
|
observed_samples,
|
||
|
|
joint_interval,
|
||
|
|
_,
|
||
|
|
joint_region_row,
|
||
|
|
) = _vcf_summary(joint_vcf)
|
||
|
|
if observed_samples != expected_samples:
|
||
|
|
raise RuntimeError("joint VCF sample header mismatch")
|
||
|
|
executable = args.gatk if args.method == "gatk" else args.bcftools
|
||
|
|
label = "GATK" if args.method == "gatk" else "bcftools"
|
||
|
|
try:
|
||
|
|
version = _tool_version(executable, label)
|
||
|
|
except Exception:
|
||
|
|
args._fallback_eligible = args.method == "gatk"
|
||
|
|
raise
|
||
|
|
parameters = {
|
||
|
|
"method": args.method,
|
||
|
|
"executable": executable,
|
||
|
|
"type_rules": (
|
||
|
|
{"SNP": "GATK SNP", "INDEL": "GATK INDEL"}
|
||
|
|
if args.method == "gatk"
|
||
|
|
else {"SNP": "bcftools snps", "INDEL": "bcftools indels"}
|
||
|
|
),
|
||
|
|
}
|
||
|
|
analysis_id = build_wgs_analysis_id(
|
||
|
|
STAGE,
|
||
|
|
[item.sha256 for values in resolved.values() for item in values],
|
||
|
|
parameters,
|
||
|
|
{args.method: version},
|
||
|
|
method=args.method,
|
||
|
|
)
|
||
|
|
attempt = workspace / ".attempts" / run_id
|
||
|
|
bundle = attempt / "bundle"
|
||
|
|
bundle.mkdir(parents=True, exist_ok=False)
|
||
|
|
base = f"{args.prefix}.{STAGE}.cohort.selected"
|
||
|
|
snp = bundle / f"{base}.snp.vcf.gz"
|
||
|
|
indel = bundle / f"{base}.indel.vcf.gz"
|
||
|
|
snp_index = Path(f"{snp}.tbi")
|
||
|
|
indel_index = Path(f"{indel}.tbi")
|
||
|
|
report = bundle / f"{args.prefix}.{STAGE}.cohort.report.md"
|
||
|
|
log_path = attempt / "variant-select.log"
|
||
|
|
with log_path.open("w", encoding="utf-8") as log:
|
||
|
|
args._fallback_eligible = args.method == "gatk"
|
||
|
|
if args.method == "gatk":
|
||
|
|
_run_logged(
|
||
|
|
[
|
||
|
|
args.gatk,
|
||
|
|
"ValidateVariants",
|
||
|
|
"-V",
|
||
|
|
str(joint_vcf),
|
||
|
|
"-L",
|
||
|
|
joint_interval,
|
||
|
|
"--validation-type-to-exclude",
|
||
|
|
"ALLELES",
|
||
|
|
"--validation-type-to-exclude",
|
||
|
|
"REF",
|
||
|
|
],
|
||
|
|
log,
|
||
|
|
"GATK ValidateVariants input",
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
_query_index(
|
||
|
|
args.bcftools,
|
||
|
|
joint_vcf,
|
||
|
|
joint_region_row,
|
||
|
|
attempt,
|
||
|
|
log,
|
||
|
|
"input",
|
||
|
|
)
|
||
|
|
for output, kind in ((snp, "SNP"), (indel, "INDEL")):
|
||
|
|
if args.method == "gatk":
|
||
|
|
_select_gatk(
|
||
|
|
args.gatk, joint_vcf, output, kind, log
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
_select_bcftools(
|
||
|
|
args.bcftools, joint_vcf, output, kind, log
|
||
|
|
)
|
||
|
|
snp_records = _postflight(
|
||
|
|
method=args.method,
|
||
|
|
gatk=args.gatk,
|
||
|
|
bcftools=args.bcftools,
|
||
|
|
output=snp,
|
||
|
|
index=snp_index,
|
||
|
|
kind="SNP",
|
||
|
|
expected_samples=expected_samples,
|
||
|
|
log=log,
|
||
|
|
)
|
||
|
|
indel_records = _postflight(
|
||
|
|
method=args.method,
|
||
|
|
gatk=args.gatk,
|
||
|
|
bcftools=args.bcftools,
|
||
|
|
output=indel,
|
||
|
|
index=indel_index,
|
||
|
|
kind="INDEL",
|
||
|
|
expected_samples=expected_samples,
|
||
|
|
log=log,
|
||
|
|
)
|
||
|
|
args._fallback_eligible = False
|
||
|
|
report.write_text(
|
||
|
|
"# WGS variant selection\n\n"
|
||
|
|
f"- method: {args.method}\n"
|
||
|
|
f"- SNP records: {snp_records}\n"
|
||
|
|
f"- INDEL records: {indel_records}\n"
|
||
|
|
"- Methods are recorded as executed; scientific equivalence is "
|
||
|
|
"not asserted.\n",
|
||
|
|
encoding="utf-8",
|
||
|
|
)
|
||
|
|
destination = (
|
||
|
|
final
|
||
|
|
/ ".wgs_variant_select_runs"
|
||
|
|
/ args.prefix
|
||
|
|
/ args.method
|
||
|
|
/ run_id
|
||
|
|
)
|
||
|
|
sources = {
|
||
|
|
"selected_snp_vcf": snp,
|
||
|
|
"selected_snp_vcf_index": snp_index,
|
||
|
|
"selected_indel_vcf": indel,
|
||
|
|
"selected_indel_vcf_index": indel_index,
|
||
|
|
"variant_select_report": report,
|
||
|
|
}
|
||
|
|
artifacts = {
|
||
|
|
role: _artifact(
|
||
|
|
workspace,
|
||
|
|
source,
|
||
|
|
destination / source.name,
|
||
|
|
role,
|
||
|
|
)
|
||
|
|
for role, source in sources.items()
|
||
|
|
}
|
||
|
|
manifest = {
|
||
|
|
"manifest_version": "1.0",
|
||
|
|
"stage": STAGE,
|
||
|
|
"status": "success",
|
||
|
|
"prefix": args.prefix,
|
||
|
|
"job_id": args.job_id,
|
||
|
|
"run_id": run_id,
|
||
|
|
"start_time": started_at,
|
||
|
|
"workspace": str(workspace),
|
||
|
|
"method": args.method,
|
||
|
|
"wgs_sample_set_id": sample_set_id,
|
||
|
|
"wgs_reference_id": reference_id,
|
||
|
|
"upstream_wgs_analysis_ids": {
|
||
|
|
"wgs_joint_genotyping": upstream_analysis_id
|
||
|
|
},
|
||
|
|
"wgs_analysis_id": analysis_id,
|
||
|
|
"parameters": parameters,
|
||
|
|
"software": {
|
||
|
|
args.method: {
|
||
|
|
"path": str(_executable_path(executable)),
|
||
|
|
"version": version,
|
||
|
|
}
|
||
|
|
},
|
||
|
|
"metrics": {
|
||
|
|
"input_sample_ids": expected_samples,
|
||
|
|
"output_sample_ids": expected_samples,
|
||
|
|
"total_samples": len(expected_samples),
|
||
|
|
"snp_records": snp_records,
|
||
|
|
"indel_records": indel_records,
|
||
|
|
},
|
||
|
|
"artifacts": artifacts,
|
||
|
|
}
|
||
|
|
manifest_work = attempt / "manifest.json"
|
||
|
|
_atomic_json(manifest_work, manifest)
|
||
|
|
if not _publish(
|
||
|
|
bundle, destination, manifest_work, authority, started_at
|
||
|
|
):
|
||
|
|
raise RuntimeError(
|
||
|
|
"stale variant-select attempt cannot replace newer method run"
|
||
|
|
)
|
||
|
|
return 0
|
||
|
|
except Exception as exc:
|
||
|
|
_publish_failure(
|
||
|
|
authority, args, run_id, started_at, str(exc)
|
||
|
|
)
|
||
|
|
print(f"{STAGE} failed: {exc}", file=sys.stderr)
|
||
|
|
return 1
|
||
|
|
|
||
|
|
|
||
|
|
def main(argv: list[str] | None = None) -> int:
|
||
|
|
return run(build_parser().parse_args(argv))
|
||
|
|
|
||
|
|
|
||
|
|
if __name__ == "__main__":
|
||
|
|
raise SystemExit(main())
|