feat: implement feature extractors for issue #82#120
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Implement RED acceptance tests for derive metric computation: - extract_cigar_ops: count M/I/D operations for CIGAR complexity - extract_allele_frequency: compute frequency for specific allele - extract_multi_map_fraction: fraction of reads multi-mapping at position Tests cover happy path, edge cases (empty inputs), and error conditions. All 24 tests registered with issue_82 prefix. 18 pass, 6 fail (RED). Failing tests identify correct multi-mapping logic not yet implemented. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- extract_cigar_ops: counts M/I/D operations from CIGAR strings - extract_allele_frequency: computes allele frequency from count maps - extract_multi_map_fraction: calculates proportion of reads with multiple alignments at a position Fixed extract_multi_map_fraction logic: counts reads that have multiple alignment records overall (indicating multi-mapping), for reads that align to the target position. Returns the fraction of multi-mapping reads among all reads at that position. All 24 feature extractor tests now pass. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
Implements the three feature extractors required for issue #82:
extract_cigar_ops(cigar: &str) → usize: Counts M/I/D operations in CIGAR strings (complexity metric)extract_allele_frequency(all_alleles: &HashMap<u8, usize>, allele: u8) → f64: Computes allele frequency from count distributionsextract_multi_map_fraction(position: u32, query_index: &QueryIndex) → f64: Calculates the fraction of reads with multiple alignments at a reference positionImplementation Details
extract_cigar_ops: Filters CIGAR string characters and counts matches (M), insertions (I), and deletions (D).
extract_allele_frequency: Divides allele count by total sum; returns 0.0 for empty maps (graceful handling).
extract_multi_map_fraction:
.len() > 1)Test Results
All 24 feature extractor tests pass:
Closes #82
🤖 Generated with Claude Code