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 Details

    • contamination

      public double contamination
  • Constructor Details

    • HaplotypeProbabilitiesFromContaminatorSequence

      public HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeBlock haplotypeBlock, double contamination)
    • HaplotypeProbabilitiesFromContaminatorSequence

      public HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeProbabilitiesFromContaminatorSequence other)
  • Method Details

    • 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
    • deepCopy

      Overrides:
      deepCopy in class HaplotypeProbabilitiesFromSequence
    • merge

      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
    • getLikelihoods

      public double[] getLikelihoods()
      Converts the loglikelihoods into linear-space with normalizing.
    • getLogLikelihoods

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

      public Snp getRepresentativeSnp()
      Simple returns the SNP from the haplotype that has the lowest genome coordinate.
      Specified by:
      getRepresentativeSnp in class HaplotypeProbabilities
    • getPosteriorProbabilities0

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

      public double[] getPosteriorProbabilities()
      getter for posteriorProbs
      Overrides:
      getPosteriorProbabilities in class HaplotypeProbabilities
    • getLikelihoods0

      public double[] getLikelihoods0()
    • 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