Package picard.fingerprint
Class HaplotypeProbabilitiesFromSequence
java.lang.Object
picard.fingerprint.HaplotypeProbabilities
picard.fingerprint.HaplotypeProbabilitiesFromSequence
- Direct Known Subclasses:
HaplotypeProbabilitiesFromContaminatorSequence
Represents the probability of the underlying haplotype given the data. By convention the
alleles stored for each SNP are in phase.
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Nested Class Summary
Nested classes/interfaces inherited from class picard.fingerprint.HaplotypeProbabilities
HaplotypeProbabilities.Genotype
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected int
protected int
protected int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
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.deepCopy()
double
double[]
Converts the loglikelihoods into linear-space with normalizing.double[]
double
Overridden to calculate the LOD from the loglikelihoods instead of the probabilities because it will allow for more accurate calculation before overflowing.double[]
Since this class uses log-rawLikelihoods natively, we override and return the native variableint
Returns the number of bases/reads that support the first allele.int
Returns the number of bases/reads that support the second allele.double[]
getter for posteriorProbsprotected double[]
Returns the posterior probability of the haplotypes given the evidence (uses the internal prior)Simple returns the SNP from the haplotype that has the lowest genome coordinate.int
Gets the total number of observations presented at this locus.boolean
Returns true if evidence has been added, false if the probabilities are just the priors.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, getPosteriorLikelihoods, getPriorProbablities, scaledEvidenceProbabilityUsingGenotypeFrequencies, shiftedLogEvidenceProbability, shiftedLogEvidenceProbabilityGivenOtherEvidence, shiftedLogEvidenceProbabilityUsingGenotypeFrequencies
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Field Details
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obsAllele1
protected int obsAllele1 -
obsAllele2
protected int obsAllele2 -
obsAlleleOther
protected int obsAlleleOther
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Constructor Details
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HaplotypeProbabilitiesFromSequence
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HaplotypeProbabilitiesFromSequence
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Method Details
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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. -
addToProbs
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 evidence is being addedbase
- the base observedqual
- the quality of the observed base
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merge
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.- Parameters:
other
- Another haplotype probabilities object to merge in- Returns:
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deepCopy
- Specified by:
deepCopy
in classHaplotypeProbabilities
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getObsAllele1
public int getObsAllele1()Returns the number of bases/reads that support the first allele.- Overrides:
getObsAllele1
in classHaplotypeProbabilities
- Returns:
- int
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getObsAllele2
public int getObsAllele2()Returns the number of bases/reads that support the second allele.- Overrides:
getObsAllele2
in classHaplotypeProbabilities
- Returns:
- int
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getTotalObs
public int getTotalObs()Gets the total number of observations presented at this locus.- Overrides:
getTotalObs
in classHaplotypeProbabilities
- Returns:
- int
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getFractionUnexpectedAlleleObs
public double getFractionUnexpectedAlleleObs() -
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) -
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() -
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) -
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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