Struct Variant 

pub struct Variant {
    pub chrom: String,
    pub position: u64,
    pub id: Option<String>,
    pub ref_allele: Vec<u8>,
    pub alt_alleles: Vec<Vec<u8>>,
    pub quality: Option<f64>,
    pub filter: VariantFilter,
}

A genomic variant (VCF-style representation).

Position is 1-based following VCF convention.

Fields

chrom: String

position: u64

1-based position (VCF convention).

id: Option<String>

Optional identifier (e.g. rs12345).

ref_allele: Vec<u8>

Reference allele.

alt_alleles: Vec<Vec<u8>>

Alternate alleles.

quality: Option<f64>

Phred-scaled quality score.

filter: VariantFilter

Filter status.

Implementations

impl Variant

pub fn new( chrom: impl Into<String>, position: u64, ref_allele: Vec<u8>, alt_alleles: Vec<Vec<u8>>, ) -> Result<Self>

Create a new variant with minimal fields.

Validates that reference and alternate alleles are non-empty.

pub fn variant_type(&self) -> VariantType

Infer the variant type from the first alternate allele.

pub fn is_snv(&self) -> bool

Whether this is a single-nucleotide variant.

pub fn is_indel(&self) -> bool

Whether this is an insertion or deletion.

pub fn is_transition(&self) -> bool

Whether this SNV is a transition (A↔G or C↔T).

Returns false for non-SNV variants.

pub fn is_transversion(&self) -> bool

Whether this SNV is a transversion (complement of transition for SNVs).

Returns false for non-SNV variants.

pub fn to_genomic_interval(&self) -> GenomicInterval

Convert the 1-based VCF position to a 0-based GenomicInterval.

The interval spans the reference allele.

Trait Implementations

impl Annotated for Variant

fn name(&self) -> &str

A human-readable name or identifier.

fn description(&self) -> Option<&str>

An optional description.

impl Clone for Variant

fn clone(&self) -> Variant

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Variant

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

Formats the value using the given formatter.

impl Scored for Variant

fn score(&self) -> f64

The score value.