2 Commits

Include renames

Author	SHA1	Message	Date
kemal	80b93e9f45	P5 validated on 2141 1000G samples; control-metric fixes (K-021) ... - Omni2.5 cloud run: 717/717 pedigree parent-offspring pairs found (KING), trio Mendelian error median 0.031 %, sex vs pedigree 99.6 %, P4 preset re-check 2138/2141 byte-identical (K-015 closed) - qc/controls: skip bead addresses absent from the IDAT; control missing only if none is on the chip - QC-008 amended: signal / zero background = +Inf (passes), 0/0 = NaN (flagged); Inf in TSV/report - plotly bundle stored gzip-compressed (repo grep stays clean: the DOM event name contains the forbidden substring) - docs: validation P5 part 2, summaries, known_unknowns K-021	2026-09-28 10:25:32 +01:00
kemal	a4c9c2d7d8	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)	2026-09-28 08:35:10 +01:00