Package picard.fingerprint
Class HaplotypeProbabilitiesFromContaminatorSequence
- java.lang.Object
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- picard.fingerprint.HaplotypeProbabilities
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- picard.fingerprint.HaplotypeProbabilitiesFromSequence
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- picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
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public class HaplotypeProbabilitiesFromContaminatorSequence extends HaplotypeProbabilitiesFromSequence
Represents the probability of the underlying haplotype of the contaminating sample given the data. 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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Field Summary
Fields Modifier and Type Field Description double
contamination
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Fields inherited from class picard.fingerprint.HaplotypeProbabilitiesFromSequence
obsAllele1, obsAllele2, obsAlleleOther
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Constructor Summary
Constructors Constructor Description HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeBlock haplotypeBlock, double contamination)
HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeProbabilitiesFromContaminatorSequence other)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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.HaplotypeProbabilitiesFromContaminatorSequence
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.HaplotypeProbabilitiesFromContaminatorSequence
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.HaplotypeProbabilitiesFromSequence
getFractionUnexpectedAlleleObs, getObsAllele1, getObsAllele2, getTotalObs, hasEvidence
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Methods inherited from class picard.fingerprint.HaplotypeProbabilities
getHaplotype, getMostLikelyGenotype, getMostLikelyHaplotype, getPosteriorLikelihoods, getPriorProbablities, scaledEvidenceProbabilityUsingGenotypeFrequencies, shiftedLogEvidenceProbability, shiftedLogEvidenceProbabilityGivenOtherEvidence, shiftedLogEvidenceProbabilityUsingGenotypeFrequencies
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Constructor Detail
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HaplotypeProbabilitiesFromContaminatorSequence
public HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeBlock haplotypeBlock, double contamination)
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HaplotypeProbabilitiesFromContaminatorSequence
public HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeProbabilitiesFromContaminatorSequence other)
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Method Detail
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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.- Overrides:
addToProbs
in classHaplotypeProbabilitiesFromSequence
- Parameters:
snp
- The snp in the HaplotypeBlock to which evidence is being addedbase
- the base observedqual
- the quality of the observed base
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deepCopy
public HaplotypeProbabilitiesFromContaminatorSequence deepCopy()
- Overrides:
deepCopy
in classHaplotypeProbabilitiesFromSequence
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merge
public HaplotypeProbabilitiesFromContaminatorSequence merge(HaplotypeProbabilities other)
Description copied from class:HaplotypeProbabilitiesFromSequence
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.- Overrides:
merge
in classHaplotypeProbabilitiesFromSequence
- Parameters:
other
- Another haplotype probabilities object to merge in
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getLikelihoods
public double[] getLikelihoods()
Converts the loglikelihoods into linear-space with normalizing.
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getLogLikelihoods
public double[] getLogLikelihoods()
Since this class uses log-rawLikelihoods natively, we override and return the native variable
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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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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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getLikelihoods0
public double[] getLikelihoods0()
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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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