Constructor Detail

• CappedHaplotypeProbabilities

  public CappedHaplotypeProbabilities​(HaplotypeProbabilities haplotypeProbabilities,
                                      double cap)

Method Detail

• 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