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 Description

HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock haplotypeBlock)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addToLogLikelihoods(Snp snp, 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()`	getter for likelihoods;
`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()`	getter for posteriors
`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,
                                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()
```
    getter for posteriors
    
    Overrides:
    
    getPosteriorProbabilities in class HaplotypeProbabilities
  - getLikelihoods
```
public double[] getLikelihoods()
```
    getter for likelihoods;
    
    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

Class HaplotypeProbabilitiesFromGenotypeLikelihoods

Nested Class Summary

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

Constructor Summary

Method Summary

Methods inherited from class picard.fingerprint.HaplotypeProbabilities

Methods inherited from class java.lang.Object

Constructor Detail

HaplotypeProbabilitiesFromGenotypeLikelihoods

Method Detail

addToLogLikelihoods

getRepresentativeSnp

hasEvidence

merge

getPosteriorProbabilities

getLikelihoods

getLogLikelihoods

setLogLikelihoods

getLodMostProbableGenotype