test(codec): read stats as fgbio KV metrics in pre-group-filter test

[nh13]

test_codec_allow_unmapped_gates_pregroup_filter parsed the codec stats file as a wide ConsensusMetrics TSV, but codec emits fgbio's vertical key-value format (ConsensusKvMetric). The header mismatch made read_tsv fail with Error parsing delimited data file header in all four cases (fast-path/threaded × default/allow-unmapped), failing test and coverage on main.

This was a semantic merge conflict, not a code regression: #513 switched codec stats to the KV format, then #509 (merged after) added this test against the old wide layout. Both merged cleanly as text, so the break only surfaced on the merged main tip — which is why the release PR (#454) and branches rebased on it (#519, #527) all inherit the same four failing cases.

The fix reads the rows back as ConsensusKvMetric and looks up the counts by key (raw_reads_considered, consensus_reads_emitted), mirroring the sibling simplex tests. The assertions' intent is unchanged: the supplementary alignment is filtered before grouping (2 raw reads considered) and the single FR molecule is emitted (1 consensus read).

Verified locally: all four cases pass; full codec module green; fmt and clippy --all-targets -D warnings clean.

Summary by CodeRabbit

• Tests
  • Updated CODEC integration test coverage to validate the current --stats tab-separated output format.
  • Added checks for raw reads considered and consensus reads emitted statistics.

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• src/lib/commands/codec.rs

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Walkthrough

The codec integration test now parses --stats output as fgbio-style seeded key-value metrics and verifies raw_reads_considered and consensus_reads_emitted.

Changes

Codec stats validation

Layer / File(s)	Summary
Update codec stats assertions src/lib/commands/codec.rs	The test imports ConsensusKvMetric, parses the stats TSV into keyed rows, and validates the expected raw-read and consensus counts.

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

Possibly related PRs

• fulcrumgenomics/fgumi#513: Refactors codec statistics to use fgbio-compatible seeded key-value metrics.
• fulcrumgenomics/fgumi#516: Adds codec-specific seeded key-value statistics and updates related expectations.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately reflects the main change: the codec test now reads stats as fgbio key-value metrics in the pre-group-filter case.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
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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• Commit unit tests in branch nh/fix-codec-stats-kv-test

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.68%. Comparing base (60dd5e7) to head (0a84e98).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #585      +/-   ##
==========================================
- Coverage   92.69%   92.68%   -0.02%     
==========================================
  Files         166      166              
  Lines      100549   100719     +170     
==========================================
+ Hits        93205    93348     +143     
- Misses       7344     7371      +27     

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[nh13]

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