picard.fingerprint

Class HaplotypeProbabilitiesFromGenotypeLikelihoods

java.lang.Object

picard.fingerprint.HaplotypeProbabilities

picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods

public class HaplotypeProbabilitiesFromGenotypeLikelihoods
extends HaplotypeProbabilities

Represents the likelihood of the HaplotypeBlock given the GenotypeLikelihoods (GL field from a VCF, which is actually a log10-likelihood) for each of the SNPs in that block. By convention the alleles stored for each SNP are in phase.

Nested Class Summary

Nested classes/interfaces inherited from class picard.fingerprint.HaplotypeProbabilities

HaplotypeProbabilities.Genotype

Constructor Summary

Constructors

Constructor and Description
HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock haplotypeBlock)

Method Summary

Modifier and Type	Method and Description
void	addToLogLikelihoods(Snp snp, java.util.List<htsjdk.variant.variantcontext.Allele> alleles, double[] logGenotypeLikelihoods) 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() Converts the loglikelihoods into linear-space.
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 variable
double[]	getPosteriorProbabilities() 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.
void	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, getObsAllele1, getObsAllele2, getPriorProbablities, getTotalObs, scaledEvidenceProbabilityUsingGenotypeFrequencies, shiftedLogEvidenceProbability, shiftedLogEvidenceProbabilityGivenOtherEvidence, shiftedLogEvidenceProbabilityUsingGenotypeFrequencies

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

HaplotypeProbabilitiesFromGenotypeLikelihoods

public HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock haplotypeBlock)

Method Detail

addToLogLikelihoods

public void addToLogLikelihoods(Snp snp,
                                java.util.List<htsjdk.variant.variantcontext.Allele> alleles,
                                double[] logGenotypeLikelihoods)

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 the likelihoods belong

alleles - the (ordered) alleles to which the biallelic genotype likelihoods correspond. So that if the alleles are [A,B], the

logGenotypeLikelihoods - correspond to the logLikelihoods of [AA, AB, BB]. Log is assumed to be in base 10.

getRepresentativeSnp

public Snp getRepresentativeSnp()

Simple returns the SNP from the haplotype that has the lowest genome coordinate.

Specified by:

getRepresentativeSnp in class HaplotypeProbabilities

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 class HaplotypeProbabilities

merge

public void 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 class HaplotypeProbabilities

Parameters:

other - Another haplotype probabilities object to merge in (must of the the same class and for the same HaplotypeBlock)

getPosteriorProbabilities

public double[] getPosteriorProbabilities()

Returns the posterior probability of the haplotypes given the evidence (uses the internal prior)

Overrides:

getPosteriorProbabilities in class HaplotypeProbabilities

getLikelihoods

public double[] getLikelihoods()

Converts the loglikelihoods into linear-space.

Specified by:

getLikelihoods in class HaplotypeProbabilities

getLogLikelihoods

public double[] getLogLikelihoods()

Since this class uses loglikelihoods natively, we override and return the native variable

Overrides:

getLogLikelihoods in class HaplotypeProbabilities

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 class HaplotypeProbabilities