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

docs/messages.md

@@ -25,6 +25,21 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `E_NO_INPUT` | error | Neither an input folder nor a sample sheet was given | CLI-006 |
 | `E_NO_INPUT_FOLDER` | error | Sample sheet has no RootFolder and no folder was given | CLI-006 |
 | `E_OUTPUT_EXISTS` | error | Outputs already exist; use --force or --resume | CLI-010 |
+| `E_QC_CONFIG_EXT` | error | QC config file must be .yaml or .yml | QC-021 |
+| `E_QC_CONFIG_MISSING` | error | QC config file does not exist | QC-021 |
+| `E_QC_CONFIG_PARSE` | error | QC config file is not valid YAML | QC-021 |
+| `E_QC_CONFIG_STRUCTURE` | error | QC config lacks the qc/report (QC/Report) wrapper | QC-021 |
+| `E_QC_DATASET_INCOMPLETE` | error | Dataset folder lacks a required file | QC-041 |
+| `E_QC_FORMAT` | error | Invalid --output-format value | QC-063 |
+| `E_QC_LABEL_COUNT` | error | Number of labels does not match number of datasets | QC-042 |
+| `E_QC_LABEL_DUPLICATE` | error | Dataset labels are not unique | QC-042 |
+| `E_QC_METHYLATION` | error | Methylation control metrics are not available yet (v2) | QC-006 |
+| `E_QC_MIXED_TYPES` | error | Genotyping and methylation datasets cannot be mixed | QC-043 |
+| `E_QC_NO_DATASETS` | error | No QC dataset folder found | QC-041 |
+| `E_QC_PROFILE` | error | Unknown QC profile | QC-024 |
+| `E_QC_THRESHOLD_KEY` | error | Unknown QC threshold key | QC-021 |
+| `E_QC_THRESHOLD_RANGE` | error | QC threshold value out of range | QC-021 |
+| `E_QC_THRESHOLD_VALUE` | error | QC threshold value is not numeric or null | QC-021 |
 | `E_SHEET_BARCODE_FORMAT` | error | Invalid SentrixBarcode_A / SentrixPosition_A value | IN-007 |
 | `E_SHEET_DELIMITER` | error | Sample sheet is not comma-delimited CSV | IN-001 |
 | `E_SHEET_DUP_COLUMN` | error | Duplicate column (column names are case-insensitive) | IN-003 |
@@ -36,6 +51,9 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `E_SHEET_RESERVED` | error | Sample sheet column collides with an output column | IN-005 |
 | `E_SHEET_TOO_LONG` | error | Sample sheet name or value longer than 500 characters | IN-006 |
 | `I_UNLISTED_IDATS` | info | IDAT pairs not listed in the sample sheet are ignored | IN-016 |
+| `W_CTRL_DEFS_DIFFER` | warning | BPM and CSV control definitions differ; the BPM wins | QC-001 |
+| `W_CTRL_MISSING` | warning | Controls needed by a metric are absent; metric not evaluable | QC-007 |
+| `W_CTRL_ZERO_DIVISOR` | warning | Control metric has a zero denominator (NaN) | QC-008 |
 | `W_DUP_IDAT_RESOLVED` | warning | Duplicate IDAT pair resolved by --on-duplicate-idat | IN-022 |
 | `W_EGT_NAME` | warning | Cluster file name is not portable | IN-045 |
 | `W_GTC_FOREIGN` | warning | GTC was produced by another tool | IN-031 |
@@ -45,6 +63,11 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `W_IDAT_NO_SCAN_TIME` | warning | IDAT has no scan entry in its run info | IN-024 |
 | `W_IDAT_UNPAIRED` | warning | IDAT channel file without its partner | IN-021 |
 | `W_MANIFEST_NO_REFSTRAND` | warning | Manifest lacks RefStrand annotation | IN-040 |
+| `W_QC_LABEL_SANITIZED` | warning | Dataset label was sanitized | QC-042 |
+| `W_QC_NO_BAF` | warning | GTC has no B-allele frequencies; contamination not estimated | QC-064 |
+| `W_QC_PEDIGREE` | warning | Parent1/Parent2/Replicate value does not name a sample in the set | IN-018 |
+| `W_QC_TOO_FEW` | warning | Too few samples or sites for a cohort QC statistic | QC-026 |
+| `W_QC_UNMATCHED_SAMPLES` | warning | Sample IDs present in one QC file but not the other | QC-040 |
 | `W_SHEET_BARCODE_REPAIRED` | warning | Barcode written as a decimal was repaired | IN-007 |
 | `W_SHEET_EMPTY_COLUMN` | warning | Columns with empty headers are ignored | IN-004 |
 | `W_SHEET_ROOTFOLDER_OVERRIDDEN` | warning | CLI folder overrides the sheet RootFolder | IN-008 |