Struct libprosic::model::priors::infinite_sites_neutral_variation::InfiniteSitesNeutralVariationModel

pub struct InfiniteSitesNeutralVariationModel {
    // some fields omitted
}

The classical population genetic model used for variant calling in e.g. GATK and Samtools.

Methods

impl InfiniteSitesNeutralVariationModel

fn new(ploidy: u32, heterozygosity: Prob) -> Self

Create new model for given ploidy and heterozygosity.

fn allele_freq_sum(ploidy: u32) -> f64

Trait Implementations

impl Model<DiscreteAlleleFreqs> for InfiniteSitesNeutralVariationModel

fn prior_prob(&self, af: AlleleFreq, _: Variant) -> LogProb

Calculate prior probability of given allele frequency.

fn joint_prob<L>(&self, afs: &DiscreteAlleleFreqs, likelihood: &L, variant: Variant) -> LogProb where L: Fn(AlleleFreq) -> LogProb

fn marginal_prob<L>(&self, likelihood: &L, variant: Variant) -> LogProb where L: Fn(AlleleFreq) -> LogProb

fn allele_freqs(&self) -> &DiscreteAlleleFreqs

Return allele frequency spectrum.