P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary

- 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)

src/simurg/formats/discovery.py

@@ -194,3 +194,19 @@ def resolve_samples(disc: Discovery, sheet: SampleSheet | None) -> tuple[list[Re
     if extra:
         notes.append(("I_UNLISTED_IDATS", f"{len(extra)} IDAT pair(s) not listed in the sample sheet are ignored"))
     return out, notes
+
+
+def discover_gtcs(root: str | Path) -> dict[str, Path]:
+    """``*.gtc`` under ``root`` keyed by file-name stem (IN-030); duplicate keys → ``E_DUP_GTC``."""
+    root = Path(root)
+    if not root.exists():
+        raise SimurgError("E_FILE_NOT_FOUND", f"GTC folder not found: {root}", path=str(root))
+    out: dict[str, Path] = {}
+    for p in walk_files(root, (".gtc",)):
+        key = p.name[: -len(".gtc")]
+        if key in out:
+            raise SimurgError("E_DUP_GTC", f"GTC files {out[key]} and {p} resolve to the same sample {key!r}")
+        out[key] = p
+    if not out:
+        raise SimurgError("E_NO_INPUT", f"no GTC files found under {root}")
+    return out