docs(dedup): stop calling the duplication ladder a saturation curve

[nh13]

The --duplication-ladder help text and the DuplicationLadderMetrics docs called the ladder a saturation curve, which it isn't.

dedup counts templates in coordinate order, and whether a template is a duplicate depends only on the other templates at its position. So the cumulative duplicate fraction after N templates is the duplicate rate of the genome covered so far. It is not the rate you'd see if the library were sequenced to N templates. A saturation curve needs templates in random order, as downsampling gives. A flattening ladder therefore doesn't mean the library is saturated, and its bumps come from regions with different duplicate rates.

This rewords the CLI help, the metric docs and the internal comments. No code changes.

Risk: Command output changes: none; unsafe changes: none, and the CLAUDE.md allowlist is unchanged; memory bounds, queue capacity, and thread/backpressure policy changes: none. Fix: clarify that the duplication ladder shows duplicate rates across templates in coordinate order, not library saturation.

Updated the --duplication-ladder help text, DuplicationLadderMetrics documentation, and internal comments to use “duplication ladder” and describe its cumulative and window fractions. No runtime behavior changes are described.

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Reviewing files that changed from the base of the PR and between fb2c977 and 917e5ed.

📒 Files selected for processing (4)

• crates/fgumi-metrics/src/dedup.rs
• src/lib/commands/dedup.rs
• src/lib/pipeline/chains/builder.rs
• src/lib/pipeline/chains/commands/dedup.rs

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Walkthrough

Documentation and comments now describe the duplication ladder as coordinate-ordered cumulative duplicate fractions that show variation across genomic regions, not sequencing-depth saturation. Runtime behavior is unchanged.

Changes

Duplication ladder documentation

Layer / File(s)	Summary
Update duplication ladder descriptions crates/fgumi-metrics/src/dedup.rs, src/lib/commands/dedup.rs, src/lib/pipeline/chains/builder.rs, src/lib/pipeline/chains/commands/dedup.rs	Metric documentation and CLI help describe cumulative duplicate fractions across coordinate-ordered templates and clarify that the ladder shows regional variation rather than saturation. Related comments use the same terminology. No executable behavior changes.

Estimated code review effort: 2 (Simple) | ~5 minutes

Suggested labels: documentation

Merge Risk: ⚪ Minimal · up to 917e5

This change clarifies the duplication ladder’s meaning without changing runtime behavior; no actionable merge risk is identified.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title uses valid conventional-commit format with the allowed type docs, the relevant dedup scope, a lowercase imperative description, and no ending period. It accurately describes the document…
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

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.13%. Comparing base (fb2c977) to head (917e5ed).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #980      +/-   ##
==========================================
- Coverage   96.15%   96.13%   -0.03%     
==========================================
  Files         293      293              
  Lines      147588   147588              
==========================================
- Hits       141919   141879      -40     
- Misses       5669     5709      +40     

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