Class HaplotypeProbabilitiesFromSequence

    • Field Detail

      • obsAllele1

        protected int obsAllele1
      • obsAllele2

        protected int obsAllele2
      • obsAlleleOther

        protected int obsAlleleOther
    • Constructor Detail

      • HaplotypeProbabilitiesFromSequence

        public HaplotypeProbabilitiesFromSequence​(HaplotypeBlock haplotypeBlock)
    • Method Detail

      • hasEvidence

        public boolean hasEvidence()
        Description copied from class: HaplotypeProbabilities
        Returns true if evidence has been added, false if the probabilities are just the priors.
      • addToProbs

        public void addToProbs​(Snp snp,
                               byte base,
                               byte qual)
        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 evidence is being added
        base - the base observed
        qual - the quality of the observed base
      • 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.
        Parameters:
        other - Another haplotype probabilities object to merge in
      • getObsAllele1

        public int getObsAllele1()
        Returns the number of bases/reads that support the first allele.
        Overrides:
        getObsAllele1 in class HaplotypeProbabilities
        Returns:
        int
      • getObsAllele2

        public int getObsAllele2()
        Returns the number of bases/reads that support the second allele.
        Overrides:
        getObsAllele2 in class HaplotypeProbabilities
        Returns:
        int
      • getTotalObs

        public int getTotalObs()
        Gets the total number of observations presented at this locus.
        Overrides:
        getTotalObs in class HaplotypeProbabilities
        Returns:
        int
      • getFractionUnexpectedAlleleObs

        public double getFractionUnexpectedAlleleObs()
      • 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