org.broadinstitute.hellbender.tools.walkers.annotator

Class InfoFieldAnnotation

java.lang.Object

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

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

All Implemented Interfaces:

Annotation

Direct Known Subclasses:

AS_InbreedingCoeff, AS_QualByDepth, AS_RMSMappingQuality, AS_StrandBiasMutectAnnotation, BaseQualityHistogram, ChromosomeCounts, CountNs, Coverage, GenotypeSummaries, MappingQualityZero, OriginalAlignment, PedigreeAnnotation, PerAlleleAnnotation, QualByDepth, RankSumTest, ReferenceBases, RMSMappingQuality, SampleList, StrandBiasTest, TandemRepeat, UniqueAltReadCount

public abstract class InfoFieldAnnotation
extends VariantAnnotation

Annotations relevant to the INFO field of the variant file (ie annotations for sites).

Constructor Summary

Constructors

Constructor and Description
InfoFieldAnnotation()

Method Summary

Modifier and Type	Method and Description
abstract java.util.Map<java.lang.String,java.lang.Object>	annotate(ReferenceContext ref, htsjdk.variant.variantcontext.VariantContext vc, AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods) Computes the annotation for the given variant and the likelihoods per read.
java.util.List<htsjdk.variant.vcf.VCFInfoHeaderLine>	getDescriptions() Returns the descriptions used for the VCF INFO meta field.

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

getKeyNames, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

InfoFieldAnnotation

public InfoFieldAnnotation()

Method Detail

annotate

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

Computes the annotation for the given variant and the likelihoods per read. Returns a map from annotation keys to values (may be empty if no annotation is to be added).

Parameters:

ref - Reference context, may be null

vc - Variant to be annotated. Not null.

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

getDescriptions

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

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