Package picard.fingerprint
Class HaplotypeProbabilitiesFromSequence
- java.lang.Object
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- picard.fingerprint.HaplotypeProbabilities
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- picard.fingerprint.HaplotypeProbabilitiesFromSequence
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- Direct Known Subclasses:
HaplotypeProbabilitiesFromContaminatorSequence
public class HaplotypeProbabilitiesFromSequence extends HaplotypeProbabilities
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
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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 protected int
obsAllele1
protected int
obsAllele2
protected int
obsAlleleOther
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Constructor Summary
Constructors Constructor Description HaplotypeProbabilitiesFromSequence(HaplotypeBlock haplotypeBlock)
HaplotypeProbabilitiesFromSequence(HaplotypeProbabilitiesFromSequence 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.HaplotypeProbabilitiesFromSequence
deepCopy()
double
getFractionUnexpectedAlleleObs()
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 variableint
getObsAllele1()
Returns the number of bases/reads that support the first allele.int
getObsAllele2()
Returns the number of bases/reads that support the second allele.double[]
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.int
getTotalObs()
Gets the total number of observations presented at this locus.boolean
hasEvidence()
Returns true if evidence has been added, false if the probabilities are just the priors.HaplotypeProbabilitiesFromSequence
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, getPosteriorLikelihoods, getPriorProbablities, scaledEvidenceProbabilityUsingGenotypeFrequencies, shiftedLogEvidenceProbability, shiftedLogEvidenceProbabilityGivenOtherEvidence, shiftedLogEvidenceProbabilityUsingGenotypeFrequencies
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Constructor Detail
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HaplotypeProbabilitiesFromSequence
public HaplotypeProbabilitiesFromSequence(HaplotypeBlock haplotypeBlock)
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HaplotypeProbabilitiesFromSequence
public HaplotypeProbabilitiesFromSequence(HaplotypeProbabilitiesFromSequence other)
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Method Detail
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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.
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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.- 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 HaplotypeProbabilitiesFromSequence 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.- Parameters:
other
- Another haplotype probabilities object to merge in- Returns:
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deepCopy
public HaplotypeProbabilitiesFromSequence 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()
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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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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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