HaplotypeProbabilitiesFromSequence (picard 2.18.2 API)

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.

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

Field Summary

Fields
Modifier and Type Field Description

protected int obsAllele1

protected int obsAllele2

protected int obsAlleleOther

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

Constructor Summary

Constructors
Constructor Description

HaplotypeProbabilitiesFromSequence(HaplotypeBlock haplotypeBlock)

Constructors
Constructor	Description
`HaplotypeProbabilitiesFromSequence(HaplotypeBlock haplotypeBlock)`

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`	`getFractionUnexpectedAlleleObs()`
`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
`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()`	getter for posteriors
`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()
```
    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 HaplotypeProbabilitiesFromSequence

Nested Class Summary

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

Field Summary

Constructor Summary

Method Summary

Methods inherited from class picard.fingerprint.HaplotypeProbabilities

Methods inherited from class java.lang.Object

Field Detail

obsAllele1

obsAllele2

obsAlleleOther

Constructor Detail

HaplotypeProbabilitiesFromSequence

Method Detail

hasEvidence

addToProbs

merge

getObsAllele1

getObsAllele2

getTotalObs

getFractionUnexpectedAlleleObs

getRepresentativeSnp

getPosteriorProbabilities

getLikelihoods

getLogLikelihoods

setLogLikelihoods

getLodMostProbableGenotype