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.

Nested Class Summary
- Nested classes/interfaces inherited from class picard.fingerprint.HaplotypeProbabilities
  HaplotypeProbabilities.Genotype

Field Summary

Fields
Modifier and Type Field Description

double contamination
- Fields inherited from class picard.fingerprint.HaplotypeProbabilitiesFromSequence
  obsAllele1, obsAllele2, obsAlleleOther

Constructor Summary

Constructors
Constructor Description

HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeBlock haplotypeBlock, double contamination)

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.
`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.
`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()
```
    getter for posteriors
    
    Overrides:
    
    getPosteriorProbabilities in class HaplotypeProbabilities
  - getLikelihoods
```
public double[] getLikelihoods()
```
    getter for likelihoods;
    
    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

Class HaplotypeProbabilitiesFromContaminatorSequence

Nested Class Summary

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

Field Summary

Fields inherited from class picard.fingerprint.HaplotypeProbabilitiesFromSequence

Constructor Summary

Method Summary

Methods inherited from class picard.fingerprint.HaplotypeProbabilitiesFromSequence

Methods inherited from class picard.fingerprint.HaplotypeProbabilities

Methods inherited from class java.lang.Object

Field Detail

contamination

Constructor Detail

HaplotypeProbabilitiesFromContaminatorSequence

Method Detail

addToProbs

merge

getLogLikelihoods

getRepresentativeSnp

getPosteriorProbabilities

getLikelihoods

setLogLikelihoods

getLodMostProbableGenotype