diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java new file mode 100755 index 000000000..2c1bb0974 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java @@ -0,0 +1,18 @@ +package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; + +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.util.List; +import java.util.Map; + +// TODO -- make this an abstract class when we move away from InfoFieldAnnotation +public interface ActiveRegionBasedAnnotation { + // return annotations for the given contexts split by sample and then allele + public abstract Map annotate(final Map>> stratifiedContexts, final VariantContext vc); + + // return the descriptions used for the VCF INFO meta field + public abstract List getDescriptions(); +} \ No newline at end of file