Package picard.fingerprint
Class CappedHaplotypeProbabilities
- java.lang.Object
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- picard.fingerprint.HaplotypeProbabilities
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- picard.fingerprint.CappedHaplotypeProbabilities
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public class CappedHaplotypeProbabilities extends HaplotypeProbabilities
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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 CappedHaplotypeProbabilities(HaplotypeProbabilities haplotypeProbabilities, double cap)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description HaplotypeProbabilities
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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CappedHaplotypeProbabilities
public CappedHaplotypeProbabilities(HaplotypeProbabilities haplotypeProbabilities, double cap)
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Method Detail
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deepCopy
public HaplotypeProbabilities 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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