kemal
c9a6173fbd
P5b: self-contained HTML QC report and QC table (simurg qc report)
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- pipeline/qc_report: dataset discovery/labels/types (QC-041..043), robust TSV/CSV reading (QC-061),
join + unmatched warning (QC-040), privacy options (QC-046), xlsx (4 sheets, conditional fills) / csv
table (QC-045), byte-deterministic HTML with gzip+base64 embedded data (QC-044, QC-047)
- qc/report: template, CSS and JS app — Control Dashboard, Automated QC (table with sort/filter/search/
paging/column menu/export, metric scatters with threshold lines), Sample Heatmaps (chip/plate,
continuous/binary), Trend Analysis (grouped summary, Tukey box plots, counts, sex, PCA), thresholds modal
(apply / download / upload YAML), linked selection across plots and table (QC-048..060)
- bundled plotly.js 2.35.2 (MIT); openpyxl dependency (MIT)
- tests: discovery/labels/errors/determinism/xlsx + headless-browser self-test
- known_unknowns K-020: remaining report deviations
2026-09-28 09:20:18 +01:00
kemal
a8caa26aa4
P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary
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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)
2026-09-28 08:35:10 +01:00
kemal
368c97b9aa
P0: project setup (packaging, CI, licences, data/oracle scripts)
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- pyproject (uv/hatch, ruff, mypy strict, pytest markers), MIT LICENSE,
THIRD_PARTY_NOTICES with verbatim BSD-2 (BeadArrayFiles) and MIT (gtc2vcf)
- CI workflow for Gitea/GitHub Actions: lint, type check, unit tests
- fetch_data.sh p0 now fetches the GSA v4 PGx demo IDATs (the GDA "Demo 36"
bundle is a GenomeStudio project), unpacks archives, fixes pipefail bug
- make_oracle_gtcs.sh builds bcftools + gtc2vcf and writes oracle GTCs
- plan §17: corrected P0 dataset table
2026-09-27 16:56:39 +01:00
kemal