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New interface for some dev work that Ryan and I are doing; only accessible from private walkers right now

This commit is contained in:
Eric Banks 2012-04-11 13:49:09 -04:00
parent dc90508104
commit 7aa654d13f
1 changed files with 18 additions and 0 deletions
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18
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java 100755
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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<String, Object> annotate(final Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, final VariantContext vc);
// return the descriptions used for the VCF INFO meta field
public abstract List<VCFInfoHeaderLine> getDescriptions();
}