feat(summary): detect binned quality scores + run-level summary-merge

[cjfields]

Summary

Adds tooling to quickly determine whether a dataset's quality scores are binned (NovaSeq/NextSeq/MiSeq i100 collapse Phred to a handful of levels) and to what levels — the starting point for analyzing binned-quality datasets.

summary: per-sample binning detection

• New always-on quality_metrics block in the JSON: distinct Q values + per-value base counts, min/max Q, is_binned, and binned_scores. Derived from the per-position histogram already computed — no extra pass over the reads.
• New flags: --binned-threshold (default 8; a file with 2–N distinct Q levels is judged binned) and --report (human-readable metrics to stderr; stdout stays clean JSON for piping).

summary-merge: run-level union report

A single low-count sample can miss rare bins (the true MiSeq i100 scheme is {2,12,24,38}, but Q2 is so rare it's often absent). The bin set is a property of the run, not a sample.

• Reads N summary JSONs and unions their observed Q values so rare bins are recovered at the run level.
• Flags per-sample bins missing from the run union (missing_from_run) — spot odd samples.
• --expected-bins 2,12,24,40 validates the run against a user-declared scheme: observed values outside the declared set are a violation (catches silent vendor scheme changes, e.g. NovaSeq v1.2 {2,12,24,40} → v1.3 {2,9,24,40}); declared-but-unobserved bins are informational.
• Vendor schemes are never hardcoded — they change without notice.

A shared judge_binned() keeps the per-sample and run-level rule identical.

Validation

• PacBio HiFi (data/dada2/samPB) → not binned, 90 distinct values.
• MiSeq i100 (11 samples) → binned, {12,24,38}; --expected-bins 2,12,24,38 reports Q2 as declared-but-unobserved (CONSISTENT); a wrong scheme yields VIOLATION.
• Synthetic A {12,24,38} + B {2,12,24,38} → run recovers {2,12,24,38}, A flagged missing Q2.
• New unit tests for judge_binned, binned/continuous detection, and count sums. Full suite (70 tests) passes.

🤖 Generated with Claude Code