Alignment executor (Case 2: reads + ref)

[crashfrog]

Parent

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

What to build

Implement AlignmentExecutor in phraya-align that orchestrates the full alignment pipeline: seed → extend (WFA) → score (multi-mapping) → record (VariantObservations + coverage_track + query_index). Handles alignment failures gracefully (log error, continue with remaining tasks).

For each query, find seeds against target, extend each seed with WFA, score all alignments, keep primary + alternatives ≥ 0.95 score ratio, extract variants from primary alignment, update coverage track, write to .phraya and .phraya.queries.

Acceptance criteria

• align_task(query: &Sequence, target: &Sequence, plan: &PhrayaPlan) → AlignmentResult
• Pipeline: find_seeds → wfa_extend for each seed → score_alignments → extract variants
• Extract VariantObservations: positions where query != target in primary alignment
• Compute local_coverage (±50bp window) from all overlapping alignments at each position
• Update coverage_track (quantize, RLE-compress)
• Write query_index (all positions + scores for this query)
• Handle failures: if WFA fails, log error, return None, don't crash
• Tests: single read, perfect match → no variants, full coverage
• Tests: single read with SNP → one VariantObservation at SNP position
• Tests: multi-mapping read → primary + alternatives in query_index
• Integration test: align 10 reads → verify output file counts

Blocked by

#74 (seed finding), #70 (WFA), #75 (multi-mapping scorer), #76 (.phraya format), #77 (.queries format)

[crashfrog]

Foundation implemented: AlignmentResult struct, basic align_task function with perfect match and SNP detection. Tests: test_perfect_match_no_variants, test_single_snp_creates_variant both passing. Next: integrate seed finding from phraya-index and WFA extension for full alignment pipeline.