fix(runall): wire --methylation-mode/--ref into the fused filter stage

[nh13]

Summary

fgumi runall's fused filter stage silently dropped the top-level --methylation-mode / --ref, so runall's methylation-aware filter option --filter::min-conversion-fraction was unreachable. build_stage_options_bag's Stage::Filter arm never threaded those flags into the filter stage the way the Simplex/Duplex arms do, so the chain builder's filter.validate_parameters() saw MethylationMode::Disabled and rejected a legitimately-set --methylation-mode — a fused … → filter chain with --methylation-mode em-seq failed with "requires --methylation-mode to be set" even though it was set.

What changed

• The Stage::Filter arm now injects the resolved methylation_mode and, when methylation is requested, the top-level reference into the projected filter options before validation (mirrors the Simplex/Duplex arms). A user-supplied --filter::ref is preserved when no top-level --ref is given.
• Filter consumes --methylation-mode only through --filter::min-conversion-fraction (the one filter option whose check reads the resolved mode; --require-strand-methylation-agreement and --min-methylation-depth use the reference/methylation tags but not the mode). So the up-front dead-flag guard treats a filter chain as a methylation consumer only when that option is set — a bare --methylation-mode on a filter chain stays rejected as inert rather than being silently accepted as a no-op.
• Renamed the methylation-gated reference helper consensus_reference → methylation_reference, now that the filter stage uses it too.

Tests

• Unit tests for the option-bag injection, the --filter::ref fallback, and both directions of the dead-flag guard (live when --filter::min-conversion-fraction is set; rejected-as-inert otherwise).
• End-to-end fused consensus → filter parity test that runs a methylation filter through runall and asserts record + header equivalence against the staged standalone simplex + filter chain.

Risk: grouping output: none; consensus output: yes for methylation-aware fused runall, pinned by staged-chain parity tests; sort order: none; corrected UMI output: none; metrics output: none. unsafe: none; CLAUDE.md allowlist: unchanged. Memory bounds, queue capacity, and thread/backpressure policy: none.

• Threads top-level --methylation-mode and --ref into fused filter stages.
• Preserves --filter::ref when no top-level reference is set.
• Rejects unused methylation options.
• Renames consensus_reference to methylation_reference.
• Adds unit and integration coverage for option wiring and fused/staged parity.

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📥 Commits

Reviewing files that changed from the base of the PR and between 1da9603 and 928deb0.

📒 Files selected for processing (2)

• src/lib/commands/runall.rs
• tests/integration/test_runall_command.rs

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---

Walkthrough

Runall now propagates top-level methylation mode and references to filter stages. Validation accepts methylation for conversion-fraction filtering and rejects inert filter-only usage. Tests cover precedence and fused versus staged execution.

Changes

Methylation wiring

Layer / File(s)	Summary
Reference propagation src/lib/commands/runall.rs	The reference helper now supports all methylation-consuming stages. Consensus and filter options receive top-level methylation settings while explicit filter references remain unchanged.
Validation and option-bag tests src/lib/commands/runall.rs	Validation recognizes --filter::min-conversion-fraction as a methylation consumer. Tests cover active and inert configurations, injection, disabled behavior, and reference precedence.
Fused consensus and filter integration tests/integration/test_runall_command.rs	The integration test compares fused simplex-consensus filtering with the equivalent staged pipeline. Documentation uses methylation_reference.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Sequence Diagram(s)

sequenceDiagram
  participant Runall
  participant SimplexConsensus
  participant Filter
  participant StagedPipeline
  Runall->>SimplexConsensus: apply top-level methylation mode and reference
  SimplexConsensus->>Filter: pass consensus output
  Runall->>Filter: inject top-level methylation options
  Filter-->>Runall: return fused filtered output
  StagedPipeline->>SimplexConsensus: run consensus stage
  StagedPipeline->>Filter: run filter with matching options
  Filter-->>StagedPipeline: return staged filtered output
  Runall->>StagedPipeline: compare records and headers

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Merge Risk: ⚪ Minimal · up to 928de

Runall now forwards top-level methylation settings to fused filter stages while preserving reference precedence and rejecting inert flags. The supplied coverage shows the fused and staged paths agree, with no merge-blocking risk remaining.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title follows the required Conventional Commit format and accurately describes wiring top-level methylation options into the fused filter stage.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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Codecov Report

❌ Patch coverage is 99.15966% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 94.37%. Comparing base (1da9603) to head (928deb0).
⚠️ Report is 5 commits behind head on main.

Files with missing lines	Patch %	Lines
src/lib/commands/runall.rs	99.15%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #944      +/-   ##
==========================================
- Coverage   94.38%   94.37%   -0.01%     
==========================================
  Files         304      304              
  Lines      150599   150713     +114     
==========================================
+ Hits       142144   142239      +95     
- Misses       8455     8474      +19     

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