perf(filter): skip the discarded full group key on the chain filter/clip paths

[nh13]

What

Unify ChainBuilder::source_group_key_config so the chain filter and clip first stages take the cheapest GroupKeyConfig::name_hash_only key at Decode time, instead of falling through to the full position/cell key (bam_group_key_config).

The full key does a per-record CIGAR 5′-position walk plus an RG/CB/MC aux-tag extraction pass. Neither filter nor clip consumes that Decode-time key — each computes what it needs itself — so on the chain path that work was computed and then discarded for every record.

This only changes a discarded key, never record bytes, so output is byte-identical to baseline.

Measured

Mac Studio (M3 Ultra, arm64), 8 threads, CPU-seconds via /usr/bin/time -l, 3 reps, byte-identical samtools view | md5 verified against baseline:

• filter — 6.0M consensus reads, -M 5 -r, ~half rejected (discarded-key path genuinely exercised): baseline 24.10 → branch 23.82 CPU-s, −1.2% (wall −1.1%). All three branch reps sit below all three baseline reps.
• clip — 18.0M mapped reads, --clip-overlapping-reads -r: flat (−0.14%, within noise). The elision is real but dwarfed by clip's NM/UQ/MD regeneration and BGZF codec. Kept in scope because it still removes dead per-record work and shares the fix below.

The win is machine-agnostic work-elision; the absolute deltas are M3-Ultra/arm64-specific.

Also fixes: a latent panic

Every arm now uses a default LibraryIndex, never from_header. name_hash_only never reads library_index, and LibraryIndex::from_header panics on a header with more than 65,535 distinct @RG libraries — so routing these stages through from_header was both pure waste and a needless crash risk.

Tests

Added filter and clip parity tests asserting byte-identical output across threading modes / against the single-threaded oracle. Full gate green (cargo ci-test/ci-fmt/ci-lint/ci-doc, plus --no-default-features / --all-features).

Risk: output remains byte-identical, pinned by filter and clip parity tests; no unsafe changes, so the CLAUDE.md allowlist is unchanged; no memory bound, queue capacity, or thread/backpressure policy changes.

• Uses GroupKeyConfig::name_hash_only for eligible chain stages.
• Avoids unnecessary CIGAR and auxiliary-tag processing.
• Removes LibraryIndex::from_header usage and its large-@RG panic risk.
• Adds filter and clip parity coverage with varied read groups, positions, and cell barcodes.
• Preserves existing sort, group routing, thread, and memory-budget coverage.

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Walkthrough

The pipeline now uses lightweight name-hash-only keys for first-stage Filter and Clip routing. Unit and integration tests verify routing and threaded parity across varied read-group, library, cell-barcode, position, and depth fields.

Changes

Group-key routing

Layer / File(s)	Summary
First-stage group-key selection src/lib/pipeline/chains/builder.rs	Filter and Clip now use name_hash_only with a default LibraryIndex. Tests verify that Group retains full key computation.
Clip threaded parity tests/integration/test_clip_command.rs	Fixtures vary RG, LB, CB, and positions. Tests compare threaded and single-threaded clipped records and normalized headers.
Filter threaded parity tests/integration/test_filter_command.rs	Fixtures vary read groups, libraries, cell barcodes, positions, and depth. Tests compare threaded and non-threaded filtered records and normalized headers.

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

Merge Risk: 🟡 Moderate · up to f7312

The Clip routing optimization lacks reliable parity coverage because the new fixture contains alignments beyond its reference bounds. Correct the fixture coordinates or reference length before merge.

Sequence Diagram(s)

sequenceDiagram
  participant Command
  participant ChainBuilder
  participant FilterOrClip
  participant ParityTest
  Command->>ChainBuilder: build threaded or single-threaded chain
  ChainBuilder->>FilterOrClip: route first-stage records with name_hash_only keys
  FilterOrClip->>ParityTest: return records and normalized header
  ParityTest->>ParityTest: compare threaded output with oracle

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🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title follows Conventional Commit format, uses the valid perf type and filter scope, and accurately describes the optimization.
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 93.54%. Comparing base (247404b) to head (f731266).
⚠️ Report is 9 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #916      +/-   ##
==========================================
- Coverage   93.55%   93.54%   -0.01%     
==========================================
  Files         301      301              
  Lines      150626   150683      +57     
==========================================
+ Hits       140923   140962      +39     
- Misses       9703     9721      +18     

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Actionable comments posted: 1

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Inline comments:
In `@tests/integration/test_clip_command.rs`:
- Around line 600-602: Adjust the fixture coordinate generation around
create_test_reference so every alignment produced by the test remains within the
200-base reference, including i == 7. Either increase the reference length or
reduce the offsets used to compute pos1 and pos2, while preserving the Clip
parity checks.

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Reviewing files that changed from the base of the PR and between 247404b and f731266.

📒 Files selected for processing (3)

• src/lib/pipeline/chains/builder.rs
• tests/integration/test_clip_command.rs
• tests/integration/test_filter_command.rs

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