Package picard.fingerprint
Class HaplotypeProbabilitiesFromGenotypeLikelihoods
- java.lang.Object
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- picard.fingerprint.HaplotypeProbabilities
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- picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
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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.
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Nested Class Summary
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Nested classes/interfaces inherited from class picard.fingerprint.HaplotypeProbabilities
HaplotypeProbabilities.Genotype
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Constructor Summary
Constructors Constructor Description HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock haplotypeBlock)
HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeProbabilitiesFromGenotypeLikelihoods other)
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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.HaplotypeProbabilitiesFromGenotypeLikelihoods
deepCopy()
double[]
getLikelihoods()
Converts the loglikelihoods into linear-space with normalizing.double[]
getLikelihoods0()
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 log-rawLikelihoods natively, we override and return the native variabledouble[]
getPosteriorProbabilities()
getter for posteriorProbsprotected double[]
getPosteriorProbabilities0()
Returns the posterior probability of the haplotypes given the evidence (uses the internal prior)Snp
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.picard.fingerprint.HaplotypeProbabilitiesUsingLogLikelihoods
merge(HaplotypeProbabilities other)
Merges information from another haplotype probabilities object for the same haplotype into this object.void
setLogLikelihoods(double[] ll)
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Methods inherited from class picard.fingerprint.HaplotypeProbabilities
getHaplotype, getMostLikelyGenotype, getMostLikelyHaplotype, getObsAllele1, getObsAllele2, getPosteriorLikelihoods, getPriorProbablities, getTotalObs, scaledEvidenceProbabilityUsingGenotypeFrequencies, shiftedLogEvidenceProbability, shiftedLogEvidenceProbabilityGivenOtherEvidence, shiftedLogEvidenceProbabilityUsingGenotypeFrequencies
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Constructor Detail
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HaplotypeProbabilitiesFromGenotypeLikelihoods
public HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock haplotypeBlock)
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HaplotypeProbabilitiesFromGenotypeLikelihoods
public HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeProbabilitiesFromGenotypeLikelihoods other)
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Method Detail
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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.
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deepCopy
public HaplotypeProbabilitiesFromGenotypeLikelihoods deepCopy()
- Specified by:
deepCopy
in classHaplotypeProbabilities
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getRepresentativeSnp
public Snp getRepresentativeSnp()
Simple returns the SNP from the haplotype that has the lowest genome coordinate.- Specified by:
getRepresentativeSnp
in classHaplotypeProbabilities
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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
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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 classHaplotypeProbabilities
- Parameters:
other
- Another haplotype probabilities object to merge in (must of the the same class and for the same HaplotypeBlock)- Returns:
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getPosteriorProbabilities0
protected double[] getPosteriorProbabilities0()
Returns the posterior probability of the haplotypes given the evidence (uses the internal prior)
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getPosteriorProbabilities
public double[] getPosteriorProbabilities()
getter for posteriorProbs- Overrides:
getPosteriorProbabilities
in classHaplotypeProbabilities
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getLikelihoods
public double[] getLikelihoods()
Converts the loglikelihoods into linear-space with normalizing.- Specified by:
getLikelihoods
in classHaplotypeProbabilities
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getLikelihoods0
public double[] getLikelihoods0()
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getLogLikelihoods
public double[] getLogLikelihoods()
Since this class uses log-rawLikelihoods natively, we override and return the native variable- Overrides:
getLogLikelihoods
in classHaplotypeProbabilities
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setLogLikelihoods
public void setLogLikelihoods(double[] ll)
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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
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