Struct AlignerWithRef 

pub struct AlignerWithRef { /* private fields */ }

Aligner with reference sequence for proper SW scoring

This aligner extracts reference sequences from the index and uses them for Smith-Waterman alignment, giving accurate scores for matches/mismatches.

Implementations

impl AlignerWithRef

pub fn new(index_with_ref: EbwtWithRef, params: AlignerParams) -> Self

Create a new aligner with reference

pub fn align(&self, read: &[Nuc], read_rc: &[Nuc]) -> AlignmentResult

Align a single read using actual reference sequences

Searches both forward and reverse complement strands and returns all valid alignments with scores computed against actual reference.

pub fn index(&self) -> &EbwtWithRef

Get the underlying EbwtWithRef