P5b: self-contained HTML QC report and QC table (simurg qc report)

- 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

docs/known_unknowns.md

@@ -4,6 +4,7 @@ Plan §20 lists the open questions; this file records what the implementation ha
 
 | ID | Date | Topic | Finding | Status |
 |---|---|---|---|---|
+| K-020 | 2026-09-28 | QC report scope (P5b) | Implemented: views A–E, linked selection, thresholds modal (apply/download/upload YAML), chip/plate heatmaps, trend table and Tukey box plots, PCA card, xlsx/csv table, privacy options, `--split-by dataset`. Not yet: client-side xlsx export (CSV only), density mode for > 12 000 points (WebGL scatter is used), `--split-by plate|run`, X/Y median R for the sex card (the summary does not carry them; the card shows the sex check instead), methylation datasets (v2). | open (deviations listed) |
 | K-019 | 2026-09-28 | GSA demo relatedness | The 36-sample GSA v4 PGx demo set contains duplicate/replicate pairs (KING φ ≈ 0.50, concordance ≥ 0.9999) and first-degree relatives (φ ≈ 0.25); without a pedigree they are flagged `duplicate_of:`/`unexpected_relatedness` as designed. Useful as a small relatedness fixture. | documented |
 | K-018 | 2026-09-28 | Locus-summary ChiTest_P100 | Against BeadArrayFiles `locus_summary.py` all columns are bit-identical on 36 GSA samples (683 054 loci) except ChiTest_P100, which differs by ≤ 3.6e-15 relative in ~15 % of loci: scipy 1.18's `ndtr` matches neither libm nor a cephes erf/erfc port bit-for-bit. Accepted (p-value). | accepted |
 | K-017 | 2026-09-28 | BAF-regression median quirk | gtc2vcf `BAFregress` (1) compares AF with the threshold as a float (0.1f), and (2) for an even number of AA/BB calls averages the quickselect result with whatever element klib `ks_ksmall` leaves just below it, not the lower middle value. Both reproduced (`--median reference`, default): 36/36 GSA samples identical to the plugin at its printed precision; `--median exact` gives the true median. SimurgArray uses autosomal sites only in pipelines; the plugin uses every VCF record. | resolved |