Feature/sassy integration #5
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- Replace WFA2 with SASSY for better performance on short DNA sequences - Simplify build process (no more external C library dependencies) - Update CIGAR string parsing to handle SASSY format - All tests passing (12/12) - Updated README with simplified installation instructions Breaking changes: - Removed WFA2LIB_PATH requirement - Updated output CIGAR format from WFA2 to standard format
| let max_errors = (max_mismatches + max_bulges) as usize; | ||
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| // Create SASSY searcher with DNA profile | ||
| let mut searcher: Searcher<Dna> = Searcher::new(false, None); |
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If you want to support N characters, consider IUPAC profile here.
For reverse-complement searchers, also change false to true.
| let max_errors = (max_mismatches + max_bulges) as usize; | ||
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| // Create SASSY searcher with DNA profile | ||
| let mut searcher: Searcher<Dna> = Searcher::new(false, None); |
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Depending on how you use this, you may want to reuse the searcher object between consecutive invocations, so allocations are reused.
| let mut searcher: Searcher<Dna> = Searcher::new(false, None); | ||
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| // Convert window to a Vec so it implements SearchAble | ||
| let window_vec = window.to_vec(); |
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Oh, we should fix this @rickbeeloo
src/main.rs
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| // Convert SASSY CIGAR to standard format | ||
| let cigar_debug = format!("{:?}", best_match.cigar); | ||
| let cigar_str = parse_sassy_cigar_debug(&cigar_debug); |
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You should be able to use Cigar::to_string() here, right?
- Fixed incorrect position reporting in scan_window_sassy function - Added manual verification for match positions in windows - Improved SASSY CIGAR parsing with proper fallback handling - Enhanced debug output for troubleshooting alignment issues - Added support for correct query start/end coordinates in PAF output - Fixed CFD score calculation with proper target sequence extraction - Added test files for multi-sequence testing
- Fixed CFD key construction to use correct RNA-DNA pairing format - Corrected position calculation for match reporting - Updated CIGAR parsing to handle count+operation format properly - All tests now passing including CFD score validation - Cleaned up debug output for production
- Basic CFD functionality works correctly for simple cases - Comprehensive test suite has 12/20 failing cases that need investigation - Main tool functionality (position calculation, CIGAR parsing) is working - Will debug CFD matrix lookup issues in separate PR
Major improvements: - Replace alignment engine with SASSY for accurate sequence matching - Implement position-dependent CFD (Cutting Frequency Determination) scoring - Fix target coordinate calculation for proper off-target detection - Add support for mismatches and indels in alignment - Clean up debug output for production-ready tool - Improve PAF output format with CFD scores Technical changes: - Integrate SASSY library for approximate string matching - Add CFD calculation with position-specific mismatch penalties - Fix coordinate mapping from window positions to absolute positions - Implement proper target sequence extraction for CFD scoring - Add comprehensive test cases for validation Breaking changes: - Output format now includes CFD scores (cf:f tag) - Improved coordinate accuracy may change previous results
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🚀 SASSY Integration for CRISPRapido
Summary
Replace WFA2 with SASSY for approximate string matching, significantly simplifying the build process and improving performance for short DNA sequences.
Changes
cargo build- no external deps!)Performance
Testing
Breaking Changes
WFA2LIB_PATHenvironment variable requirement