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.
-
-
Nested Class Summary
-
Nested classes/interfaces inherited from class picard.fingerprint.HaplotypeProbabilities
HaplotypeProbabilities.Genotype
-
-
Constructor Summary
Constructors Constructor Description HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock haplotypeBlock)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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.double[]
getLikelihoods()
getter for likelihoods;double
getLodMostProbableGenotype()
Overridden to calculate the LOD from the loglikelihoods instead of the probabilities because it will allow for more accurate calculation before overflowing.double[]
getLogLikelihoods()
Since this class uses loglikelihoods natively, we override and return the native variabledouble[]
getPosteriorProbabilities()
getter for posteriorsSnp
getRepresentativeSnp()
Simple returns the SNP from the haplotype that has the lowest genome coordinate.boolean
hasEvidence()
Returns true if evidence has been added, false if the probabilities are just the priors.void
merge(HaplotypeProbabilities other)
Merges information from another haplotype probabilities object for the same haplotype into this object.void
setLogLikelihoods(double[] ll)
-
Methods inherited from class picard.fingerprint.HaplotypeProbabilities
getHaplotype, getMostLikelyGenotype, getMostLikelyHaplotype, getObsAllele1, getObsAllele2, getPriorProbablities, getTotalObs, scaledEvidenceProbabilityUsingGenotypeFrequencies, shiftedLogEvidenceProbability, shiftedLogEvidenceProbabilityGivenOtherEvidence, shiftedLogEvidenceProbabilityUsingGenotypeFrequencies
-
-
-
-
Constructor Detail
-
HaplotypeProbabilitiesFromGenotypeLikelihoods
public HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock haplotypeBlock)
-
-
Method Detail
-
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 belongalleles
- the (ordered) alleles to which the biallelic genotype likelihoods correspond. So that if the alleles are [A,B], thelogGenotypeLikelihoods
- correspond to the logLikelihoods of [AA, AB, BB]. Log is assumed to be in base 10.
-
getRepresentativeSnp
public Snp getRepresentativeSnp()
Simple returns the SNP from the haplotype that has the lowest genome coordinate.- Specified by:
getRepresentativeSnp
in classHaplotypeProbabilities
-
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 classHaplotypeProbabilities
-
merge
public void 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 classHaplotypeProbabilities
- Parameters:
other
- Another haplotype probabilities object to merge in (must of the the same class and for the same HaplotypeBlock)
-
getPosteriorProbabilities
public double[] getPosteriorProbabilities()
getter for posteriors- Overrides:
getPosteriorProbabilities
in classHaplotypeProbabilities
-
getLikelihoods
public double[] getLikelihoods()
getter for likelihoods;- Specified by:
getLikelihoods
in classHaplotypeProbabilities
-
getLogLikelihoods
public double[] getLogLikelihoods()
Since this class uses loglikelihoods natively, we override and return the native variable- Overrides:
getLogLikelihoods
in classHaplotypeProbabilities
-
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 classHaplotypeProbabilities
-
-