org.broadinstitute.hellbender.tools.walkers.annotator

Class PerAlleleAnnotation

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation

org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation

org.broadinstitute.hellbender.tools.walkers.annotator.PerAlleleAnnotation

All Implemented Interfaces:

Annotation

Direct Known Subclasses:

BaseQuality, FragmentLength, MappingQuality, ReadPosition

public abstract class PerAlleleAnnotation
extends InfoFieldAnnotation

Apply an annotation based on aggregation data from all reads supporting each allele.

Constructor Summary

Constructors

Constructor and Description
PerAlleleAnnotation()

Method Summary

Modifier and Type	Method and Description
protected abstract int	aggregate(java.util.List<java.lang.Integer> values)
java.util.Map<java.lang.String,java.lang.Object>	annotate(ReferenceContext ref, htsjdk.variant.variantcontext.VariantContext vc, AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods) Calculate annotations for each allele based on given VariantContext and likelihoods for a given genotype's sample and add the annotations to the GenotypeBuilder.
protected abstract java.lang.String	getDescription()
java.util.List<htsjdk.variant.vcf.VCFInfoHeaderLine>	getDescriptions() Returns the descriptions used for the VCF INFO meta field.
java.util.List<java.lang.String>	getKeyNames() Return the keys
protected abstract java.util.OptionalInt	getValueForRead(GATKRead read, htsjdk.variant.variantcontext.VariantContext vc)
protected abstract java.lang.String	getVcfKey()
protected boolean	includeRefAllele()

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation

toString

Methods inherited from class java.lang.Object

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

Constructor Detail

PerAlleleAnnotation

public PerAlleleAnnotation()

Method Detail

annotate

public java.util.Map<java.lang.String,java.lang.Object> annotate(ReferenceContext ref,
                                                                 htsjdk.variant.variantcontext.VariantContext vc,
                                                                 AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods)

Calculate annotations for each allele based on given VariantContext and likelihoods for a given genotype's sample and add the annotations to the GenotypeBuilder. By default annotations are only calculated for alt alleles but implementations may override the includeRefAllele() method. See parent class docs in GenotypeAnnotation.

Specified by:

annotate in class InfoFieldAnnotation

Parameters:

ref - Reference context, may be null

vc - Variant to be annotated. Not null.

likelihoods - likelihoods indexed by sample, allele, and read within sample

includeRefAllele

protected boolean includeRefAllele()

getDescriptions

public java.util.List<htsjdk.variant.vcf.VCFInfoHeaderLine> getDescriptions()

Description copied from class: InfoFieldAnnotation

Returns the descriptions used for the VCF INFO meta field. Subclasses must ensure that this list is not null and does not contain null.

Overrides:

getDescriptions in class InfoFieldAnnotation

getKeyNames

public java.util.List<java.lang.String> getKeyNames()

Description copied from class: VariantAnnotation

Return the keys

Specified by:

getKeyNames in class VariantAnnotation

getValueForRead

protected abstract java.util.OptionalInt getValueForRead(GATKRead read,
                                                         htsjdk.variant.variantcontext.VariantContext vc)

aggregate

protected abstract int aggregate(java.util.List<java.lang.Integer> values)

getVcfKey

protected abstract java.lang.String getVcfKey()

getDescription

protected abstract java.lang.String getDescription()