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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]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
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kemalandClaude Opus 5.5 committed 2026-09-28 09:20:18 +01:00
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THIRD_PARTY_NOTICES.md
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@@ -7,6 +7,8 @@ used only as external subprocess oracles and are not copied or linked.
|---|---|---|
| [Illumina BeadArrayFiles](https://github.com/Illumina/BeadArrayFiles) — Copyright (c) 2020, Illumina | BSD-2-Clause | File-format layouts (GTC, BPM, EGT), normalization-bin rule, `GTC_File_Format_v5.pdf`; locus-summary formulas (`examples/locus_summary.py`, ported to `simurg/qc/locus_summary.py`); test oracle |
| [gtc2vcf / idat2gtc](https://github.com/freeseek/gtc2vcf) — Copyright (C) 2018-2025 Giulio Genovese | MIT | IDAT field codes, BPM locus-entry order, EGT data-block variants, GTC write order, assay-type inference (`infer_assay_type`); BAF-regression numerics (`BAFregress.c`, `simurg/qc/contamination.py`); test oracle |
| [plotly.js](https://github.com/plotly/plotly.js) 2.35.2 — Copyright (c) 2021 Plotly, Inc | MIT | Bundled verbatim in `simurg/qc/report/vendor/plotly.min.js` and inlined into QC reports (licence files alongside) |
| [openpyxl](https://foss.heptapod.net/openpyxl/openpyxl) | MIT | Runtime dependency: `.xlsx` QC table (not vendored) |
| [klib `ksort.h`](https://github.com/attractivechaos/klib) as shipped in htslib — Copyright (c) 2008, 2012-2013, 2017-2019 Genome Research Ltd | MIT | Quickselect `ks_ksmall` partition order, ported to `simurg/qc/contamination.py` (`ks_ksmall`) to reproduce BAFregress medians |
| [Illumina GTCtoVCF](https://github.com/Illumina/GTCtoVCF) | Apache-2.0 | VCF conversion rules (phase P6) |
| [Picard `picard.arrays`](https://github.com/broadinstitute/picard) | MIT | Second format reference |