org.broadinstitute.hellbender.tools.walkers.mutect

Class SubsettedLikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix<EVIDENCE,A>

All Implemented Interfaces:

AlleleList<A>, LikelihoodMatrix<EVIDENCE,A>

public class SubsettedLikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>
extends java.lang.Object
implements LikelihoodMatrix<EVIDENCE,A>

Fast wrapper for a LikelihoodMatrix that uses only a subset of alleles. Useful for model comparison of different allele subsets without having to copy the underlying likelihoods. Created by davidben on 1/26/17.

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.AlleleList

EMPTY_LIST

Constructor Summary

Constructors

Constructor and Description
SubsettedLikelihoodMatrix(LikelihoodMatrix<EVIDENCE,A> matrix, java.util.List<A> alleles)

Method Summary

Modifier and Type	Method and Description
java.util.List<A>	alleles() List of alleles in the matrix sorted by their index in the collection.
static boolean	basesMatch(htsjdk.variant.variantcontext.Allele a, htsjdk.variant.variantcontext.Allele b)
void	copyAlleleLikelihoods(int alleleIndex, double[] dest, int offset) Copies the likelihood of all the evidence for a given allele into an array from a particular offset.
java.util.List<EVIDENCE>	evidence() List of evidence in the matrix sorted by their index therein.
int	evidenceCount() Count of evidence in the matrix.
static <EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele> SubsettedLikelihoodMatrix<EVIDENCE,A>	excludingAllele(LikelihoodMatrix<EVIDENCE,A> matrix, htsjdk.variant.variantcontext.Allele excludedAllele)
double	get(int alleleIndex, int evidenceIndex) Returns the likelihood of a unit of evidence given a haplotype.
A	getAllele(int alleleIndex) Returns the allele given its index.
EVIDENCE	getEvidence(int evidenceIndex) Returns the allele given its index.
int	indexOfAllele(A allele) Queries the index of an allele in the matrix.
int	indexOfEvidence(EVIDENCE evidence) Queries the index of a unit of evidence in the matrix.
int	numberOfAlleles() Number of allele in the matrix.
void	set(int alleleIndex, int evidenceIndex, double value) Set the likelihood of a unit of evidence given an allele through their indices.

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.AlleleList

asListOfAlleles, containsAllele, emptyAlleleList, equals, indexOfReference, permutation

Constructor Detail

SubsettedLikelihoodMatrix

public SubsettedLikelihoodMatrix(LikelihoodMatrix<EVIDENCE,A> matrix,
                                 java.util.List<A> alleles)

Method Detail

excludingAllele

public static <EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele> SubsettedLikelihoodMatrix<EVIDENCE,A> excludingAllele(LikelihoodMatrix<EVIDENCE,A> matrix,
                                                                                                                                                                     htsjdk.variant.variantcontext.Allele excludedAllele)

basesMatch

public static boolean basesMatch(htsjdk.variant.variantcontext.Allele a,
                                 htsjdk.variant.variantcontext.Allele b)

evidence

public java.util.List<EVIDENCE> evidence()

Description copied from interface: LikelihoodMatrix

List of evidence in the matrix sorted by their index therein.

Specified by:

evidence in interface LikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

Returns:

never null.

alleles

public java.util.List<A> alleles()

Description copied from interface: LikelihoodMatrix

List of alleles in the matrix sorted by their index in the collection.

Specified by:

alleles in interface LikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

Returns:

never null.

set

public void set(int alleleIndex,
                int evidenceIndex,
                double value)

Description copied from interface: LikelihoodMatrix

Set the likelihood of a unit of evidence given an allele through their indices.

Specified by:

set in interface LikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

Parameters:

alleleIndex - the target allele index.

evidenceIndex - the target evidence index.

value - new likelihood value for the target evidence give the target allele.

get

public double get(int alleleIndex,
                  int evidenceIndex)

Description copied from interface: LikelihoodMatrix

Returns the likelihood of a unit of evidence given a haplotype.

Specified by:

get in interface LikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

Parameters:

alleleIndex - the index of the given haplotype.

evidenceIndex - the index of the target evidence.

Returns:

the requested likelihood, whatever value was provided using set or 0.0 if none was set.

indexOfAllele

public int indexOfAllele(A allele)

Description copied from interface: LikelihoodMatrix

Queries the index of an allele in the matrix.

Specified by:

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

Specified by:

indexOfAllele in interface LikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

Parameters:

allele - the target allele.

Returns:

-1 if such allele does not exist, otherwise its index which 0 or greater.

indexOfEvidence

public int indexOfEvidence(EVIDENCE evidence)

Description copied from interface: LikelihoodMatrix

Queries the index of a unit of evidence in the matrix.

Specified by:

indexOfEvidence in interface LikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

Parameters:

evidence - the target evidence.

Returns:

-1 if there is not such a evidence in the matrix, otherwise its index which is 0 or greater.

numberOfAlleles

public int numberOfAlleles()

Description copied from interface: LikelihoodMatrix

Number of allele in the matrix.

Specified by:

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

Specified by:

numberOfAlleles in interface LikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

Returns:

never negative.

evidenceCount

public int evidenceCount()

Description copied from interface: LikelihoodMatrix

Count of evidence in the matrix.

Specified by:

evidenceCount in interface LikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

Returns:

never negative.

getAllele

public A getAllele(int alleleIndex)

Description copied from interface: LikelihoodMatrix

Returns the allele given its index.

Specified by:

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

Specified by:

getAllele in interface LikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

Parameters:

alleleIndex - the target allele index.

Returns:

never null.

getEvidence

public EVIDENCE getEvidence(int evidenceIndex)

Description copied from interface: LikelihoodMatrix

Returns the allele given its index.

Specified by:

getEvidence in interface LikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

Parameters:

evidenceIndex - the target allele index.

Returns:

never null.

copyAlleleLikelihoods

public void copyAlleleLikelihoods(int alleleIndex,
                                  double[] dest,
                                  int offset)

Description copied from interface: LikelihoodMatrix

Copies the likelihood of all the evidence for a given allele into an array from a particular offset.

Specified by:

copyAlleleLikelihoods in interface LikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

Parameters:

alleleIndex - the targeted allele

dest - the destination array.

offset - the copy offset within the destination allele