kemal
a8caa26aa4
- qc/controls: canonical control names (QC-002), bkg/offset (QC-003), 13 genotyping metrics (QC-004/005), missing/zero-divisor handling (QC-007/008); controls_raw.tsv / controls_qc.tsv (QC-009/011) incl. compat CSVs - qc/thresholds + profiles: YAML schema, validation codes, precedence, shipped profiles, auto (QC-020..025) - qc/status: functional PASS/FAIL/NA, control CLEAR/FLAGGED, flags (QC-030..033) - qc/contamination: BAF regression; bit-compatible with gtc2vcf BAFregress (36/36, K-017), exact mode too - qc/relatedness: KING-robust, duplicates, Mendelian errors, pedigree from sheet (IN-018) - qc/locus_summary: OUT-072, bit-identical to BeadArrayFiles except ChiTest (K-018) - qc/suggest: suggest-thresholds (QC-026) - pipeline/qc: disk-backed cohort store; CLI qc controls|samples|contamination|relatedness|loci|suggest-thresholds - genotype: control tables (OUT-070), het_rate, QC columns, cohort QC - tests: unit + oracle (BAFregress plugin, BeadArrayFiles locus summary)
118 lines
3.9 KiB
Python
118 lines
3.9 KiB
Python
"""Two-axis sample QC status and informational flags (spec QC-030, QC-031, QC-033, QC-034).
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* functional status (PASS/FAIL/NA) — call rate and LogR deviation only;
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* control status (CLEAR/FLAGGED) — control-probe metrics including the assay control;
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* flags — informational, never change either status.
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"""
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from __future__ import annotations
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import math
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from collections.abc import Mapping, Sequence
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from dataclasses import dataclass, field
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from typing import Any
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import numpy as np
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from simurg.qc.thresholds import CONTROL_KEYS, KEY_TO_COLUMN, Thresholds
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CONTAMINATION_FLAG = 0.02 # plan §9.3 [OURS]
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HET_Z = 3.0
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ASSAY_CONTROL_MIN = 1.0 # OUT-062
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@dataclass
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class SampleStatus:
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functional_status: str = "NA"
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control_status: str = ""
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control_flag_codes: list[str] = field(default_factory=list)
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na_metrics: list[str] = field(default_factory=list)
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flags: list[str] = field(default_factory=list)
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def columns(self) -> dict[str, str]:
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return {
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"functional_status": self.functional_status,
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"control_status": self.control_status,
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"control_flag_codes": ";".join(self.control_flag_codes),
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"flags": ";".join(self.flags),
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}
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def _num(v: Any) -> float:
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try:
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return float(v)
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except (TypeError, ValueError):
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return math.nan
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def functional_status(row: Mapping[str, Any] | None, th: Thresholds) -> str:
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"""QC-030. ``row`` is a sample-summary row; None means no genotyping summary (NA)."""
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if row is None:
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return "NA"
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if row.get("status", "OK") != "OK":
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return "FAIL"
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cr, ld = th.get("callRate"), th.get("logRDev")
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if cr.fails(_num(row.get("autosomal_call_rate"))) or ld.fails(_num(row.get("logr_dev"))):
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return "FAIL"
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return "PASS"
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def control_status(
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values: Mapping[str, float] | None, na_metrics: Sequence[str], th: Thresholds
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) -> tuple[str, list[str]]:
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"""QC-031: FLAGGED iff an enabled, evaluable control metric is out of range. Codes in QC-004 order."""
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if values is None:
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return "", []
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codes = []
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for key in CONTROL_KEYS:
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col = KEY_TO_COLUMN[key]
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t = th.get(key)
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if not t.enabled or col not in values or col in na_metrics:
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continue
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if t.fails(_num(values[col])):
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codes.append(key)
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return ("FLAGGED" if codes else "CLEAR"), codes
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def het_zscores(het: Sequence[float]) -> list[float]:
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"""z-scores of heterozygosity within the batch (NaN where undefined or with < 3 finite values)."""
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a = np.array([_num(h) for h in het], dtype=np.float64)
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ok = np.isfinite(a)
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if ok.sum() < 3:
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return [math.nan] * len(a)
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mu, sd = float(a[ok].mean()), float(a[ok].std(ddof=1))
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if sd == 0:
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return [0.0 if o else math.nan for o in ok]
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return [float((x - mu) / sd) if o else math.nan for x, o in zip(a, ok, strict=True)]
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def sample_flags(
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row: Mapping[str, Any],
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th: Thresholds,
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*,
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het_z: float = math.nan,
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probe_columns: Sequence[str] = (),
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duplicates: Sequence[str] = (),
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unexpected_relatedness: bool = False,
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) -> list[str]:
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"""QC-033 flags in a fixed order."""
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flags: list[str] = []
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ok = row.get("status", "OK") == "OK"
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if ok and th.get("callRate").fails(_num(row.get("autosomal_call_rate"))):
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flags.append("low_call_rate")
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if ok and th.get("logRDev").fails(_num(row.get("logr_dev"))):
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flags.append("high_lrr_sd")
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if row.get("sex_check") == "mismatch":
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flags.append("sex_mismatch")
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if math.isfinite(het_z) and abs(het_z) > HET_Z:
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flags.append("het_outlier")
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c = _num(row.get("contamination"))
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if math.isfinite(c) and c > CONTAMINATION_FLAG:
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flags.append("contaminated")
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if ok and any(_num(row.get(p)) < ASSAY_CONTROL_MIN for p in probe_columns):
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flags.append("assay_control_fail")
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flags.extend(f"duplicate_of:{d}" for d in duplicates)
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if unexpected_relatedness:
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flags.append("unexpected_relatedness")
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return flags
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