Class HaplotypeProbabilitiesFromContaminatorSequence


  • public class HaplotypeProbabilitiesFromContaminatorSequence
    extends HaplotypeProbabilitiesFromSequence
    Represents the probability of the underlying haplotype of the contaminating sample given the data. By convention the alleles stored for each SNP are in phase.
    • Field Detail

      • contamination

        public double contamination
    • Constructor Detail

      • HaplotypeProbabilitiesFromContaminatorSequence

        public HaplotypeProbabilitiesFromContaminatorSequence​(HaplotypeBlock haplotypeBlock,
                                                              double contamination)
    • Method Detail

      • 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.
        Overrides:
        addToProbs in class HaplotypeProbabilitiesFromSequence
        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)
        Description copied from class: HaplotypeProbabilitiesFromSequence
        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.
        Overrides:
        merge in class HaplotypeProbabilitiesFromSequence
        Parameters:
        other - Another haplotype probabilities object to merge in
      • getLogLikelihoods

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