picard.fingerprint

Class HaplotypeProbabilitiesFromContaminatorSequence

java.lang.Object

picard.fingerprint.HaplotypeProbabilities

picard.fingerprint.HaplotypeProbabilitiesFromSequence

picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence

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.

Author:

Yossi Farjoun

Nested Class Summary

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

HaplotypeProbabilities.Genotype

Field Summary

Fields

Modifier and Type	Field and Description
double	contamination

Fields inherited from class picard.fingerprint.HaplotypeProbabilitiesFromSequence

obsAllele1, obsAllele2, obsAlleleOther

Constructor Summary

Constructors

Constructor and Description
HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeBlock haplotypeBlock, double contamination)

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[]	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.
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.HaplotypeProbabilitiesFromSequence

getFractionUnexpectedAlleleObs, getObsAllele1, getObsAllele2, getTotalObs, hasEvidence

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

contamination

public double contamination

Constructor Detail

HaplotypeProbabilitiesFromContaminatorSequence

public HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeBlock haplotypeBlock,
                                                      double contamination)

Method Detail

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 class HaplotypeProbabilitiesFromSequence

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)

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 class HaplotypeProbabilitiesFromSequence

Parameters:

other - Another haplotype probabilities object to merge in

getLogLikelihoods

public double[] getLogLikelihoods()

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

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

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