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/qc/control_names.yaml

@@ -0,0 +1,84 @@
+# Canonical control-probe IDs (spec QC-002). Keys are *normalised* names: case-folded, whitespace collapsed,
+# no spaces next to or inside parentheses, "bgnd" written as "bkg". Several manifest spellings map to one ID.
+canonical:
+  # staining
+  biotin(high): biotin_high
+  biotin(bkg): biotin_bkg
+  biotin(5k): biotin_5k
+  dnp(high): dnp_high
+  dnp(bkg): dnp_bkg
+  dnp(20k): dnp_20k
+  # extension
+  extension(a): ext_A
+  extension(t): ext_T
+  extension(c): ext_C
+  extension(g): ext_G
+  # hybridization
+  hyb(high): hyb_high
+  hyb(medium): hyb_medium
+  hyb(low): hyb_low
+  # target removal
+  target removal: target_removal_1
+  target removal(1): target_removal_1
+  target removal 1: target_removal_1
+  target removal(2): target_removal_2
+  target removal 2: target_removal_2
+  # stringency
+  string(pm): string_pm
+  string(mm): string_mm
+  # non-specific binding (one bead type per colour label on genotyping chips)
+  nsb(bkg): nsb_bkg
+  nsb(bkg) red: nsb_bkg
+  nsb(bkg) green: nsb_bkg
+  nsb(bkg) blue: nsb_bkg
+  nsb(bkg) purple: nsb_bkg
+  # non-polymorphic
+  np(a): np_A
+  np(t): np_T
+  np(c): np_C
+  np(g): np_G
+  # restoration (FFPE)
+  restoration: restoration
+  restore: restoration
+  # methylation (metrics in v2; names mapped already so controls_raw.tsv is labelled consistently)
+  bs conversion i c1: bs1_C1
+  bs conversion i c2: bs1_C2
+  bs conversion i c3: bs1_C3
+  bs conversion i c4: bs1_C4
+  bs conversion i c5: bs1_C5
+  bs conversion i u1: bs1_U1
+  bs conversion i u2: bs1_U2
+  bs conversion i u3: bs1_U3
+  bs conversion i u4: bs1_U4
+  bs conversion i u5: bs1_U5
+  bs conversion ii-1: bs2_1
+  bs conversion ii-2: bs2_2
+  bs conversion ii-3: bs2_3
+  bs conversion ii-4: bs2_4
+  gt mismatch 1(pm): gtmm_1_pm
+  gt mismatch 2(pm): gtmm_2_pm
+  gt mismatch 3(pm): gtmm_3_pm
+  gt mismatch 4(pm): gtmm_4_pm
+  gt mismatch 5(pm): gtmm_5_pm
+  gt mismatch 6(pm): gtmm_6_pm
+  gt mismatch 1(mm): gtmm_1_mm
+  gt mismatch 2(mm): gtmm_2_mm
+  gt mismatch 3(mm): gtmm_3_mm
+  gt mismatch 4(mm): gtmm_4_mm
+  gt mismatch 5(mm): gtmm_5_mm
+  gt mismatch 6(mm): gtmm_6_mm
+  specificity 1: spec2_1
+  specificity 2: spec2_2
+  specificity 3: spec2_3
+
+# Categories treated as methylation-only (dataset type detection, QC-043).
+methylation_categories:
+  - bisulfite conversion i
+  - bisulfite conversion ii
+  - specificity i
+  - specificity ii
+
+# Report exclusion list (QC-010): raw-probe views leave these out; derived metrics still use them.
+report_exclude:
+  categories: [negative, norm]
+  names: ["np(g) 1", "np(g) 2", "np(g) 3", "np(g) 4", "np(g) 5", "biotin(5k)", "dnp(20k)"]