Class CappedHaplotypeProbabilities

    • Constructor Detail

      • CappedHaplotypeProbabilities

        public CappedHaplotypeProbabilities​(HaplotypeProbabilities haplotypeProbabilities,
                                            double cap)
    • Method Detail

      • merge

        public picard.fingerprint.HaplotypeProbabilitiesUsingLogLikelihoods 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)
        Returns:
      • getPosteriorProbabilities0

        protected double[] getPosteriorProbabilities0()
        Returns the posterior probability of the haplotypes given the evidence (uses the internal prior)
      • getLikelihoods0

        public double[] getLikelihoods0()
      • getLogLikelihoods

        public double[] getLogLikelihoods()
        Since this class uses log-rawLikelihoods 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