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/methylation_msa.yaml

@@ -0,0 +1,25 @@
+# Methylation MSA profile (spec QC-024). Methylation metrics are computed from v2 on.
+qc:
+  report:
+    stainingGreen: 5
+    stainingRed: 5
+    extensionGreen: 5
+    extensionRed: 5
+    hybGreenHighMed: 1
+    hybGreenMediumLow: 1
+    targetRemovalI: 1
+    targetRemovalII: 1
+    restoration: 0
+    npGreen: 2.5
+    npRed: 3
+    bisulfiteConversionIGreen: 1
+    bisulfiteConversionIRed: 1
+    bisulfiteConversionIGreenBg: 0.5
+    bisulfiteConversionIRedBg: 0.5
+    bisulfiteConversionII: 0.5
+    bisulfiteConversionIIBg: 0.5
+    specificityIGreen: 1
+    specificityIRed: 1
+    specificityII: 1
+    specificityIIBg: 1
+    bgOffset: 3000