* simurg/core/brand.py: single source of the mark geometry, colours, favicon
and the report header band (scripts/brand now load it from there).
* HTML reports (QC report, compare dashboard, methylation QC): offline SVG
favicon, indigo header band with the mark, version and a sha256 of the data
shown; Noto Sans font stack; methylation plots in Okabe-Ito colours.
* README banner, guide logo, brand/blog links; branding brief updated to the
final identity; Noto (OFL) and Okabe-Ito entries in THIRD_PARTY_NOTICES;
CHANGELOG (Unreleased).
Unit tests + P5 QC oracle: 285 passed; ruff and mypy clean.
Methylation CSV manifest reader (MET-002/003), raw M/U assembly with bead masking
(MET-005), pOOBAH detection p-values, noob background correction, linear/nonlinear dye
bias, beta and M-values (MET-010..012), the 21 methylation control metrics (MET-006,
bs-conv red-bg set option), per-sample ctrl/cgs tables, summary tsv/xlsx/html with the
detection histogram and a beta PCA, pcs.tsv.gz, controls_raw/controls_qc.tsv; methylation
datasets load in qc report (MET-014); qc controls --array-type methylation; minfi-style
Sentrix_ID/Sentrix_Position sheet keys. Vendor EPIC manifests carry a 5th field on some
control lines: >= 4 fields accepted. Runs on the public minfiDataEPIC set (3 x NA12878).
- 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
kemal