[TEST] #70: WFA extension (scalar)

[crashfrog]

Summary

• Comprehensive test suite for scalar WFA extension (issue WFA extension (scalar) #70)
• 56 unit tests covering all acceptance criteria
• 9 criterion benchmarks for 10kb alignment performance baseline
• Full TDD RED phase validation

Test Coverage

API Validation

• Function signature: wfa_extend(query, target, seed_pos) → Alignment
• Alignment struct fields: edit_distance, query/target positions, CIGAR

Functional Tests

• Exact matches (100bp perfect alignment)
• Single mismatches with CIGAR validation
• Single insertions with 'I' in CIGAR
• Single deletions with 'D' in CIGAR
• Complex alignments (mixed M/I/D operations)
• Empty sequence handling

Edge Cases

• Single base sequences
• Very long indels (50bp)
• Seed position variants (start, middle, end)
• CIGAR format validation
• Edit distance bounds checking

Benchmarks

• 10kb exact match
• 10kb with 1%, 5%, 10% divergence
• Varying sequence lengths (100bp to 10kb)
• Varying divergence levels (0% to 20%)
• Different seed positions

Test Status

RED PHASE (as expected):

• 112 compilation errors
• Tests define API from acceptance criteria
• Current implementation has different signature
• Implementation agent will make tests pass (GREEN phase)

Files Added

1. tests/test_wfa_scalar_acceptance.rs - 56 unit tests
2. benches/bench_wfa_scalar.rs - 9 benchmarks
3. TEST_PLAN_ISSUE_70.md - Test plan documentation

Blocker Status

Issue #59 (error types): RESOLVED - WfaError exists

Next Steps

Implementation agent should:

1. Update Alignment struct (add edit_distance, positions)
2. Update wfa_extend signature (seed_pos: usize)
3. Implement scalar WFA algorithm
4. Verify all 56 tests pass
5. Run benchmarks for 10kb baseline

Generated with Claude Code

[crashfrog]

Closing stale PR. Work has been superseded or merged via alternative approach.