Class HaplotypeProbabilitiesFromGenotypeLikelihoods


  • public class HaplotypeProbabilitiesFromGenotypeLikelihoods
    extends HaplotypeProbabilities
    Represents the likelihood of the HaplotypeBlock given the GenotypeLikelihoods (GL field from a VCF, which is actually a log10-likelihood) for each of the SNPs in that block. By convention the alleles stored for each SNP are in phase.
    • Constructor Detail

      • HaplotypeProbabilitiesFromGenotypeLikelihoods

        public HaplotypeProbabilitiesFromGenotypeLikelihoods​(HaplotypeBlock haplotypeBlock)
    • Method Detail

      • addToLogLikelihoods

        public void addToLogLikelihoods​(Snp snp,
                                        List<htsjdk.variant.variantcontext.Allele> alleles,
                                        double[] logGenotypeLikelihoods)
        Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
        Parameters:
        snp - The snp in the haplotypeblock to which the likelihoods belong
        alleles - the (ordered) alleles to which the biallelic genotype likelihoods correspond. So that if the alleles are [A,B], the
        logGenotypeLikelihoods - correspond to the logLikelihoods of [AA, AB, BB]. Log is assumed to be in base 10.
      • merge

        public void merge​(HaplotypeProbabilities other)
        Merges information from another haplotype probabilities object for the same haplotype into this object. Useful for when probabilities need to be merged to levels higher than the read group, e.g. the sample or individual.
        Specified by:
        merge in class HaplotypeProbabilities
        Parameters:
        other - Another haplotype probabilities object to merge in (must of the the same class and for the same HaplotypeBlock)
      • getLogLikelihoods

        public double[] getLogLikelihoods()
        Since this class uses loglikelihoods natively, we override and return the native variable
        Overrides:
        getLogLikelihoods in class HaplotypeProbabilities
      • setLogLikelihoods

        public void setLogLikelihoods​(double[] ll)
      • getLodMostProbableGenotype

        public double getLodMostProbableGenotype()
        Overridden to calculate the LOD from the loglikelihoods instead of the probabilities because it will allow for more accurate calculation before overflowing.
        Overrides:
        getLodMostProbableGenotype in class HaplotypeProbabilities