Package picard.fingerprint

Class CappedHaplotypeProbabilities

java.lang.Object
picard.fingerprint.HaplotypeProbabilities
picard.fingerprint.CappedHaplotypeProbabilities
public class CappedHaplotypeProbabilities extends HaplotypeProbabilities

  • Constructor Details

    • CappedHaplotypeProbabilities

      public CappedHaplotypeProbabilities(HaplotypeProbabilities haplotypeProbabilities, double cap)

  • Method Details

    • deepCopy

      public HaplotypeProbabilities deepCopy()
      Specified by:
      deepCopy in class HaplotypeProbabilities

    • getRepresentativeSnp

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

    • hasEvidence

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

    • 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)

    • getPosteriorProbabilities

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

    • getLikelihoods

      public double[] getLikelihoods()
      Converts the loglikelihoods into linear-space with normalizing.
      Specified by:
      getLikelihoods in class HaplotypeProbabilities

    • 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