Struct Alignment 

pub struct Alignment {
    pub bwt_row: u64,
    pub seed_offset: usize,
    pub ref_start: usize,
    pub ref_end: usize,
    pub score: Score,
    pub strand: Strand,
    pub edits: usize,
    pub cigar: String,
    pub md: String,
    pub edit_ops: Vec<EditOp>,
    pub seed_hit_count: usize,
}

A single alignment result

Fields

bwt_row: u64

BWT row position (unresolved genome coordinate)

seed_offset: usize

Offset of the seed within the read

ref_start: usize

Starting position in reference

ref_end: usize

Ending position in reference

score: Score

Alignment score

strand: Strand

Strand (forward or reverse)

edits: usize

Number of edits (mismatches + indels)

cigar: String

CIGAR string

md: String

MD:Z tag (mismatch string)

edit_ops: Vec<EditOp>

Edit operations

seed_hit_count: usize

Number of genome positions the seed matched (lower = more unique)

Implementations

impl Alignment

pub fn new( ref_start: usize, ref_end: usize, score: Score, strand: Strand, ) -> Self

Create a new alignment

Trait Implementations

impl Clone for Alignment

fn clone(&self) -> Alignment

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Alignment

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for Alignment

fn default() -> Alignment

Returns the “default value” for a type.