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)
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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.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.void
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, 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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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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merge
public void 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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getLogLikelihoods
public double[] getLogLikelihoods()
Since this class uses loglikelihoods 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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getPosteriorProbabilities
public double[] getPosteriorProbabilities()
getter for posteriors- Overrides:
getPosteriorProbabilities
in classHaplotypeProbabilities
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getLikelihoods
public double[] getLikelihoods()
getter for likelihoods;- Specified by:
getLikelihoods
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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