2 Commits

Include renames

Author	SHA1	Message	Date
kemal	c1fcb088c5	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	2026-09-28 10:25:32 +01:00
kemal	c9a6173fbd	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	2026-09-28 09:20:18 +01:00