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

README.md

@@ -12,7 +12,11 @@ Personal research toolkit for Illumina Infinium genotyping BeadChip data
 Phases **P0 (setup)**, **P1 (file parsers)**, **P2 (canonical model, raw X/Y)**, **P3 (normalization)** and **P4 (genotype
 calling, GTC output)** are complete — see `docs/validation/`. Each is validated on 2141 vendor GTCs of the 1000 Genomes Omni2.5 set
 (normalization bit-identical; genotypes/scores identical in 2138/2141 samples).
-Available commands: `simurg version`, `simurg inspect <files…> [--json]`, `simurg ingest`, `simurg normalize`, `simurg genotype`.
+Phase **P5 (QC)** is in progress: control-probe metrics, thresholds/profiles, two-axis sample status, BAF-regression
+contamination, KING-robust relatedness, Mendelian errors and the locus summary are implemented and match their open-source
+references on the GSA demo set (`docs/validation/P5.md`); the cohort-scale validation and the HTML report are pending.
+Available commands: `simurg version`, `simurg inspect <files…> [--json]`, `simurg ingest`, `simurg normalize`, `simurg genotype`,
+`simurg qc controls|samples|contamination|relatedness|loci|suggest-thresholds`.
 
 ## Quick start
 
@@ -22,6 +26,7 @@ uv run pytest tests/unit                  # no downloads needed
 bash scripts/bootstrap_refs.sh            # reference open-source repos → refs/ (oracles)
 bash scripts/fetch_data.sh p0             # ~1.4 GB of public test data → data/
 bash scripts/make_oracle_gtcs.sh          # builds gtc2vcf, writes oracle GTCs
+bash scripts/make_oracle_qc.sh            # locus-summary oracle (BeadArrayFiles, separate venv)
 uv run pytest tests/oracle                # real-data acceptance tests (add -m "not slow" to skip the long ones)
 uv run simurg inspect data/p0/gsa_v4_pgx/idats_Demo_36/idats_Demo_36/207895980019/207895980019_R03C01_Grn.idat
 ```