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U-M6s-01 RED batch adjudications (T1 → T2 GREEN handoff)

Source: vignettes/articles/devlog-2026-10-07-m6s-red-adjudication.qmd

The RED batch (test(m6s): ms_hrd_report RED 批次…, cherry-picked as 038ec43) was authored strictly against the design memo (vignettes/articles/devlog-2026-10-07-m6s-hrd-report-design.qmd, §1/§2/§3.3). The dry-run is all-red for the intended reason ('ms_hrd_report' is not an exported object), and every hand-derived golden reproduces under the verbatim SigMiner oracle in tests/testthat/helper-hrd.R. Nine points where the memo was silent were flagged for adjudication; resolutions below bind the GREEN batch (T2). Where the memo is authoritative, the memo wins unchanged.

1. Segment column layout — memo §2 confirmed

Input frame columns are sample/chromosome/start/end/state/minor_cn/caller/assay (memo §2). The seg_median_ratio/tumor_purity/cellularity fields do not feed either verbatim score and are not required nor validated by ms_hrd_report(). GREEN must not add hidden dependencies on them.

2. Error topics — memo verbatim + package convention

Verbatim gates keep the memo topics exactly: hrd-wes-experimental (WES assay) and hrd-caller-whitelist (non-whitelisted caller). Malformed input and unsupported genome build follow the established msuiter_abort topics input and genome (cf. io-segments precedent). GREEN adopts these and no others.

3. Return-column spellings — ratified

ploh_fraction (normalised pLOH score), aneuploidy_count (non-zero-flag autosomes), hrd_score (composite; see §4). RED pins presence/type; these spellings are now the API contract.

4. Composite hrd_score — pinned for GREEN with provenance

hrd_score = 1L iff ploh_fraction >= 0.4 and aneuploidy_count >= 4 (Cortes-Castro convention). Provenance to be cited in both the implementation docstring and the memo amendment: Cortes-Castro et al., Cancer Research 2020, which defines the combined pLOH + aneuploidy classifier with these cut-offs. GREEN must (a) verify the exact bibliographic record and the cut-offs against the primary source before citing it, and (b) add the numeric golden block to test-hrd-reference.R before flipping the assertion; the RED batch deliberately carries no numeric pin here (no-invent rule).

5. Geometry injection — ratify dots, refdb supplies defaults in GREEN

Reference geometry (arm table, centromere-equivalent spans, ploidy, chr_size) is injectable via ... for test determinism (RED relies on this). GREEN sources production defaults from refdb (get_cn_ploidy, hg19 build table) so that a plain ms_hrd_report(seg) call needs no geometry arguments. Injected values always win over refdb defaults.

6. Whole-chrom fraction/2 — RED reading confirmed

Memo verbatim “whole-chrom split fraction/2” means each of the two arms of a whole-chromosome-covered autosome carries fraction = 0.5 (summing to 1.0 per chromosome), so flag = as.integer(round(sum(state * fraction) - ploidy[1])) is computed over the two half-weight arms. This matches the memo §1 replay; the 0.5 per-arm convention is ratified.

7. Blacklist scope — p-arms only, skip-not-scored

Blacklist {13, 14, 15, 21, 22} applies to their p-arms only (memo §1 verbatim; the task’s looser “chromosome” wording is superseded). An autosome whose only covered arm is a blacklisted p-arm contributes nothing (is skipped), rather than scoring round(0 - ploidy). RED encodes exactly this.

8. Diagnostic columns — GREEN defines, RED pins shape only

n_windows_scored (count over injected geometry’s window binning), coverage_note, ploidy_source (enum: "user" when ploidy injected, else refdb-derived path). Numeric semantics arrive with GREEN alongside the refdb wiring of §5; RED asserts presence/type/enum only.

9. Caller casing — lowercase exact-match with input normalisation

The whitelist is the five lowercase labels {battenberg, ascat, facets, purple, sequenza}. GREEN normalises the caller argument to lowercase before comparison (documented behaviour); case-sensitivity of the stored labels is not part of the contract. Unknown/nonstring caller still hits hrd-caller-whitelist per §2.

GREEN batch entry conditions (T2)

  1. §4 composite numeric golden added first (test-first discipline preserved).
  2. Implementation lives in R/hrd-report.R; docs via roxygen with usethis/devtools workflow; docs-sync guard must pass.
  3. Full repo-mode testthat suite green including the 33 RED blocks; R CMD check --as-cran gate per CI contract.
  4. Phase PR merges the whole feat branch (design memo + RED + GREEN) as one big-phase PR per the PR mandate.