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RustAlign Alignment Algorithms
This crate implements the seed-based alignment and Smith-Waterman dynamic programming algorithms used by RustAlign.
Structs§
- Aligner
- Main aligner that orchestrates seed search and DP extension
- Aligner
Params - Parameters for the aligner
- Aligner
With Ref - Aligner with reference sequence for proper SW scoring
- Alignment
- A single alignment result
- Alignment
Result - Result of aligning a read
- Constraint
- Constraints on alignment edits
- Paired
Alignment - Result of a paired-end alignment
- PeConstraints
- Paired-end constraints
- Query
Profile - Query profile for SIMD alignment
- Seed
- A seed (substring match) for alignment
- Seed
Aligner - Seed aligner that searches for seed matches
- Seed
Policy - Seed policy configuration
- Seed
Results - Results from seed search
- SwAligner
- Smith-Waterman aligner with banded DP
- SwParams
- Parameters for Smith-Waterman alignment
- SwSse
Aligner - SIMD-accelerated Smith-Waterman aligner
Enums§
- PeAlignment
Type - Classification of paired-end alignment types
- PePolicy
- Paired-end orientation policy
- Seed
Type - Seed types for alignment