picard.fingerprint

Class HaplotypeProbabilitiesFromSequence

java.lang.Object

picard.fingerprint.HaplotypeProbabilities

picard.fingerprint.HaplotypeProbabilitiesFromSequence

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.

Author:

Tim Fennell

Nested Class Summary

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

HaplotypeProbabilities.Genotype

Field Summary

Fields

Modifier and Type	Field and Description
protected int	obsAllele1
protected int	obsAllele2
protected int	obsAlleleOther

Constructor Summary

Constructors

Constructor and Description
HaplotypeProbabilitiesFromSequence(HaplotypeBlock haplotypeBlock)

Method Summary

Modifier and Type	Method and 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	getFractionUnexpectedAlleleObs()
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
int	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() 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.
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, getPriorProbablities, scaledEvidenceProbabilityUsingGenotypeFrequencies, shiftedLogEvidenceProbability, shiftedLogEvidenceProbabilityGivenOtherEvidence, shiftedLogEvidenceProbabilityUsingGenotypeFrequencies

Methods inherited from class java.lang.Object

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

Field Detail

obsAllele1

protected int obsAllele1

obsAllele2

protected int obsAllele2

obsAlleleOther

protected int obsAlleleOther

Constructor Detail

HaplotypeProbabilitiesFromSequence

public HaplotypeProbabilitiesFromSequence(HaplotypeBlock haplotypeBlock)

Method Detail

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

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 added

base - the base observed

qual - the quality of the observed base

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.

Parameters:

other - Another haplotype probabilities object to merge in

getObsAllele1

public int getObsAllele1()

Returns the number of bases/reads that support the first allele.

Overrides:

getObsAllele1 in class HaplotypeProbabilities

Returns:

int

getObsAllele2

public int getObsAllele2()

Returns the number of bases/reads that support the second allele.

Overrides:

getObsAllele2 in class HaplotypeProbabilities

Returns:

int

getTotalObs

public int getTotalObs()

Gets the total number of observations presented at this locus.

Overrides:

getTotalObs in class HaplotypeProbabilities

Returns:

int

getFractionUnexpectedAlleleObs

public double getFractionUnexpectedAlleleObs()

getRepresentativeSnp

public Snp getRepresentativeSnp()

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

Specified by:

getRepresentativeSnp in class HaplotypeProbabilities

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