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

scripts/make_oracle_gtcs.sh

@@ -9,14 +9,14 @@ cd "$(dirname "$0")/.."
 V=1.22
 T=refs/tools
 B=$T/bcftools-$V
-if [[ ! -x $B/bcftools || ! -f $B/plugins/idat2gtc.so ]]; then
+if [[ ! -x $B/bcftools || ! -f $B/plugins/idat2gtc.so || ! -f $B/plugins/BAFregress.so ]]; then
   [[ -d refs/gtc2vcf ]] || bash scripts/bootstrap_refs.sh
   mkdir -p $T
   [[ -f $T/bcftools.tar.bz2 ]] || curl -sL -o $T/bcftools.tar.bz2 \
     "https://github.com/samtools/bcftools/releases/download/$V/bcftools-$V.tar.bz2"
   tar -xjf $T/bcftools.tar.bz2 -C $T
-  rm -f $B/plugins/{idat2gtc,gtc2vcf,affy2vcf}.{c,h}
-  cp refs/gtc2vcf/{idat2gtc,gtc2vcf,affy2vcf}.c refs/gtc2vcf/*.h $B/plugins/
+  rm -f $B/plugins/{idat2gtc,gtc2vcf,affy2vcf,BAFregress}.{c,h}
+  cp refs/gtc2vcf/{idat2gtc,gtc2vcf,affy2vcf,BAFregress}.c refs/gtc2vcf/*.h $B/plugins/
   (cd $B/htslib-$V && ./configure --disable-libcurl --disable-bz2 --disable-lzma --disable-ref-cache >/dev/null)
   (cd $B && ./configure --without-gsl >/dev/null && make -j"$(nproc)" CFLAGS="-g -O2 -ffp-contract=off" >/dev/null)
 fi