Package picard.fingerprint

Class HaplotypeProbabilitiesFromGenotypeLikelihoods

java.lang.Object
picard.fingerprint.HaplotypeProbabilities
picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
public class HaplotypeProbabilitiesFromGenotypeLikelihoods extends HaplotypeProbabilities
Represents the likelihood of the HaplotypeBlock given the GenotypeLikelihoods (GL field from a VCF, which is actually a log10-likelihood) for each of the SNPs in that block. By convention the alleles stored for each SNP are in phase.

  • Constructor Details

  • Method Details

    • addToLogLikelihoods

      public void addToLogLikelihoods(Snp snp, List<htsjdk.variant.variantcontext.Allele> alleles, double[] logGenotypeLikelihoods)
      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.
      Parameters:
      snp - The snp in the haplotypeblock to which the likelihoods belong
      alleles - the (ordered) alleles to which the biallelic genotype likelihoods correspond. So that if the alleles are [A,B], the
      logGenotypeLikelihoods - correspond to the logLikelihoods of [AA, AB, BB]. Log is assumed to be in base 10.

    • deepCopy

      public HaplotypeProbabilitiesFromGenotypeLikelihoods 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