phraya filter CLI

[crashfrog]

Parent

#58 (Phase 1 MVP: Evidence-Informed Alignment with Deferred Filtering)

What to build

Implement `phraya filter` CLI command in phraya-cli. Reads .phraya file, applies threshold filters, outputs VCF/TSV/filtered-phraya format. Supports chaining: filtered .phraya can be input to another filter invocation. Enables exploring different filter parameters without re-alignment.

Acceptance criteria

• `phraya filter <input.phraya> [--min-coverage N] [--max-coverage N] [--min-mapq N] [--format vcf|tsv|phraya]`
• Read .phraya file
• Apply configured filters using FilterBuilder
• Output to stdout in specified format (default: VCF)
• Format=phraya: write filtered .phraya file (subset of observations)
• Support chaining: `phraya filter --min-coverage 10 | phraya filter --min-mapq 30` (when format=phraya)
• Log filter statistics to stderr (e.g., "Filtered 1000 → 850 observations")
• Return non-zero exit code on error
• Integration test: align → filter --min-coverage 10 → verify VCF output
• Integration test: align → filter → filter (chain) → verify TSV output
• Integration test: filter --format phraya → verify output is valid .phraya file

Blocked by

#81 (filter library), #83 (VCF formatter), #84 (TSV formatter)

[crashfrog]

Resolved by #112

Note: Implementation 9/13 tests passing. Threshold-related tests need review.