org.broadinstitute.hellbender.tools.walkers.genotyper

Class GenotypingData<A extends htsjdk.variant.variantcontext.Allele>

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData<A>

All Implemented Interfaces:

AlleleList<A>, SampleList

public final class GenotypingData<A extends htsjdk.variant.variantcontext.Allele>
extends java.lang.Object
implements SampleList, AlleleList<A>

Encapsulates the data use to make the genotype calls.

Nested Class Summary

Nested classes/interfaces inherited from interface org.broadinstitute.hellbender.utils.genotyper.AlleleList

AlleleList.ActualPermutation<A extends htsjdk.variant.variantcontext.Allele>, AlleleList.NonPermutation<A extends htsjdk.variant.variantcontext.Allele>

Field Summary

Fields inherited from interface org.broadinstitute.hellbender.utils.genotyper.SampleList

EMPTY_LIST

Fields inherited from interface org.broadinstitute.hellbender.utils.genotyper.AlleleList

EMPTY_LIST

Constructor Summary

Constructors

Constructor and Description
GenotypingData(PloidyModel ploidyModel, ReadLikelihoods<A> likelihoods) Constructs a new genotyping-data collection providing the ploidy model to apply to the input model and the read-likelihoods collection.

Method Summary

Modifier and Type	Method and Description
A	getAllele(int index) Returns the allele at the given index in this AlleleList.
java.lang.String	getSample(int sampleIndex) Returns the element given its index within the set.
int	indexOfAllele(A allele) Returns the index of the given Allele in this AlleleList.
int	indexOfSample(java.lang.String sample) Returns the index of an object.
int	numberOfAlleles() Returns the number of alleles in this AlleleList.
int	numberOfSamples() Returns number of elements in the list.
PloidyModel	ploidyModel() Returns the ploidy model that corresponds to the data provided.
ReadLikelihoods<A>	readLikelihoods() Returns read-likelihoods to use for genotyping.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.broadinstitute.hellbender.utils.genotyper.SampleList

asListOfSamples, asSetOfSamples, emptySampleList, equals, singletonSampleList

Methods inherited from interface org.broadinstitute.hellbender.utils.genotyper.AlleleList

asListOfAlleles, containsAllele, emptyAlleleList, equals, indexOfReference, permutation

Constructor Detail

GenotypingData

public GenotypingData(PloidyModel ploidyModel,
                      ReadLikelihoods<A> likelihoods)

Constructs a new genotyping-data collection providing the ploidy model to apply to the input model and the read-likelihoods collection.

Parameters:

ploidyModel - the ploidy model.

likelihoods - the read-likelihoods collection.

Throws:

java.lang.IllegalArgumentException - if either ploidyModel or likelihoods is null, or they are not compatible in terms of the samples they contain; their lists must match.

Method Detail

ploidyModel

public PloidyModel ploidyModel()

Returns the ploidy model that corresponds to the data provided.

Returns:

never null.

numberOfSamples

public int numberOfSamples()

Description copied from interface: SampleList

Returns number of elements in the list.

Specified by:

numberOfSamples in interface SampleList

indexOfSample

public int indexOfSample(java.lang.String sample)

Description copied from interface: SampleList

Returns the index of an object.

Specified by:

indexOfSample in interface SampleList

Parameters:

sample - the sample of interest.

Returns:

-1 if such a sample is not an element of this set, otherwise is index in the set thus a values within [0,SampleList.numberOfSamples()).

getSample

public java.lang.String getSample(int sampleIndex)

Description copied from interface: SampleList

Returns the element given its index within the set.

Specified by:

getSample in interface SampleList

Parameters:

sampleIndex - the target samples's index.

Returns:

never null; as null is not a valid element.

readLikelihoods

public ReadLikelihoods<A> readLikelihoods()

Returns read-likelihoods to use for genotyping.

Returns:

never null.

numberOfAlleles

public int numberOfAlleles()

Description copied from interface: AlleleList

Returns the number of alleles in this AlleleList.

Specified by:

numberOfAlleles in interface AlleleList<A extends htsjdk.variant.variantcontext.Allele>

indexOfAllele

public int indexOfAllele(A allele)

Description copied from interface: AlleleList

Returns the index of the given Allele in this AlleleList. Returns a negative number if the given allele is not present in this AlleleList.

Specified by:

indexOfAllele in interface AlleleList<A extends htsjdk.variant.variantcontext.Allele>

getAllele

public A getAllele(int index)

Description copied from interface: AlleleList

Returns the allele at the given index in this AlleleList.

Specified by:

getAllele in interface AlleleList<A extends htsjdk.variant.variantcontext.Allele>