kemalandClaude Opus 5.5 0c004f6398 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

2026-09-28 08:35:10 +01:00

..

test_p1_real_files.py

P1: file parsers, sample sheet, discovery, CLI inspect

2026-09-27 16:56:39 +01:00

test_p2_raw_xy.py

P3: normalization fit (1.2.0 and 1.1.2), apply, polar, simurg normalize

2026-09-27 22:51:06 +01:00

test_p3_normalization.py

P3: normalization fit (1.2.0 and 1.1.2), apply, polar, simurg normalize

2026-09-27 22:51:06 +01:00

test_p4_genotype.py

P4 (WIP): GenCall-equivalent calling, BAF/LRR, sex, GTC v5, simurg genotype

2026-09-28 00:07:37 +01:00

test_p5_qc.py

P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary

2026-09-28 08:35:10 +01:00