Package picard.fingerprint

Class HaplotypeProbabilitiesFromSequence

java.lang.Object
picard.fingerprint.HaplotypeProbabilities
picard.fingerprint.HaplotypeProbabilitiesFromSequence
Direct Known Subclasses:
HaplotypeProbabilitiesFromContaminatorSequence
public class HaplotypeProbabilitiesFromSequence extends HaplotypeProbabilities
Represents the probability of the underlying haplotype given the data. By convention the alleles stored for each SNP are in phase.

  • Field Details

    • obsAllele1

      protected int obsAllele1

    • obsAllele2

      protected int obsAllele2

    • obsAlleleOther

      protected int obsAlleleOther

  • Constructor Details

  • Method Details

    • hasEvidence

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

    • 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.
      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 HaplotypeProbabilitiesFromSequence 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.
      Parameters:
      other - Another haplotype probabilities object to merge in
      Returns:

    • deepCopy

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

    • getObsAllele1

      public int getObsAllele1()
      Returns the number of bases/reads that support the first allele.
      Overrides:
      getObsAllele1 in class HaplotypeProbabilities
      Returns:
      int

    • getObsAllele2

      public int getObsAllele2()
      Returns the number of bases/reads that support the second allele.
      Overrides:
      getObsAllele2 in class HaplotypeProbabilities
      Returns:
      int

    • getTotalObs

      public int getTotalObs()
      Gets the total number of observations presented at this locus.
      Overrides:
      getTotalObs in class HaplotypeProbabilities
      Returns:
      int

    • getFractionUnexpectedAlleleObs

      public double getFractionUnexpectedAlleleObs()

    • 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

    • 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