kemal and Claude Opus 5.5
fbc4080a50
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
Co-Authored-By: Claude Opus 5.5 <[email protected] https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
2026-09-28 09:20:18 +01:00
kemal and Claude Opus 5.5
a4faead6d7
P2 (WIP): raw X/Y assembly, canonical Parquet model, simurg ingest
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- signal/raw_xy.py: vectorised Infinium I/II raw X/Y and control assembly
(plan §7.1) with a per-chip address-map cache; IN-027 coverage gate
- core/schemas.py: Arrow schemas (loci, sample_intensity, controls),
deterministic atomic Parquet writing
- pipeline/ingest.py + CLI: discovery, sheet, IN-010 naming, overwrite
check before any work, spawn-based workers, per-sample isolation,
--resume by input hashes, run manifest, exit codes 0/3/4
- matches gtc2vcf raw X/Y and controls exactly on 18 GSA samples;
outputs byte-identical across thread counts and layouts
Co-Authored-By: Claude Opus 5.5 <[email protected] https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
2026-09-27 20:54:06 +01:00
kemal and Claude Opus 5.5
f10c651f0f
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
Co-Authored-By: Claude Opus 5.5 <[email protected] https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
2026-09-27 16:56:39 +01:00
kemalandClaude Opus 5.5