Struct VariantCaller 

pub struct VariantCaller { /* private fields */ }

Variant caller that processes pileup data to call SNPs

Implementations

impl VariantCaller

pub fn new(config: VariantCallerConfig) -> Self

Create a new variant caller with the given configuration

pub fn call_snp( &self, pileup: &PileupColumn, reference_base: u8, ) -> Option<VariantCall>

Call a SNP at a single pileup position

Returns Some(VariantCall) if a variant is detected, None if all reads match the reference or depth is insufficient.

pub fn call_indel( &self, pileup: &PileupColumn, reference_base: u8, next_ref_bases: &[u8], ) -> Option<VariantCall>

Detect insertions/deletions from pileup data

Looks for gaps (represented as b’-’) in the pileup bases that indicate indels relative to the reference.

pub fn filter_variants(&self, calls: &mut [VariantCall])

Apply quality and depth filters to a list of variant calls

pub fn to_vcf(&self, calls: &[VariantCall], sample_name: &str) -> String

Generate VCF-formatted output for variant calls