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Author SHA1 Message Date
kemalandClaude Opus 5.5 c1c2c30c87 v2 methylation control QC (WIP): simurg methyl qc|convert-manifest (MET-001..018)
ci / test (3.12) (push) Failing after 8s
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ci / test (3.13) (push) Failing after 10s
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Methylation CSV manifest reader (MET-002/003), raw M/U assembly with bead masking
(MET-005), pOOBAH detection p-values, noob background correction, linear/nonlinear dye
bias, beta and M-values (MET-010..012), the 21 methylation control metrics (MET-006,
bs-conv red-bg set option), per-sample ctrl/cgs tables, summary tsv/xlsx/html with the
detection histogram and a beta PCA, pcs.tsv.gz, controls_raw/controls_qc.tsv; methylation
datasets load in qc report (MET-014); qc controls --array-type methylation; minfi-style
Sentrix_ID/Sentrix_Position sheet keys. Vendor EPIC manifests carry a 5th field on some
control lines: >= 4 fields accepted. Runs on the public minfiDataEPIC set (3 x NA12878).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 00:13:22 +01:00
kemalandClaude Opus 5.5 60a05d5048 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

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-28 10:25:32 +01:00
kemalandClaude Opus 5.5 0c004f6398 P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary
ci / test (3.12) (push) Failing after 8s
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ci / test (3.13) (push) Failing after 11s
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- 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