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)

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

src/simurg/qc/profiles/genotyping_example.yaml

@@ -0,0 +1,20 @@
+# Alternative example values from the reference documentation (spec QC-024). Starting point for review only.
+qc:
+  report:
+    callRate: 0.98
+    logRDev: 0.15
+    stainingGreen: 5
+    stainingRed: 5
+    extensionGreen: 5
+    extensionRed: 5
+    hybGreenHighMed: 1.25
+    hybGreenMediumLow: 1.25
+    targetRemovalI: 5
+    restoration: null
+    stringency: 1.5
+    nonSpecificBindingGreen: 5
+    nonSpecificBindingRed: 5
+    npGreen: 5
+    npRed: 5
+    assayControl: 1
+    bgOffset: 3000