Case 4 alignment (contigs only)

[crashfrog]

Parent

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

What to build

Extend AlignmentExecutor to support Case 4: M contigs with or without reference. If reference provided, align M contigs to reference (M tasks). If no reference, perform all-vs-all MSA (M×(M-1)/2 tasks, or M-1 if centroid used).

This is the minimap2-like use case for comparing assembled genomes.

Acceptance criteria

• Case 4 with reference: M alignment tasks (each contig → reference)
• Case 4 without reference (MSA): M×(M-1)/2 tasks (all pairs) or use centroid (M-1 tasks)
• Tests: 5 contigs + reference → 5 tasks
• Tests: 5 contigs, no reference → 10 tasks (all-vs-all) or 4 tasks (centroid mode)
• Integration test: plan (case 4 with ref) → align all → verify outputs
• Integration test: plan (case 4 MSA) → align all → merge → verify

Blocked by

#78 (alignment executor)