diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java index a8c622a96..03c7d279b 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java @@ -27,12 +27,11 @@ package org.broadinstitute.sting.utils; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; @@ -41,6 +40,7 @@ public class Haplotype { protected final double[] quals; private GenomeLoc genomeLocation = null; private HashMap readLikelihoodsPerSample = null; + private HashMap eventMap = null; private boolean isRef = false; private Cigar cigar; private int alignmentStartHapwrtRef; @@ -97,6 +97,14 @@ public class Haplotype { return readLikelihoodsPerSample.keySet(); } + public HashMap getEventMap() { + return eventMap; + } + + public void setEventMap( final HashMap eventMap ) { + this.eventMap = eventMap; + } + public boolean isReference() { return isRef; }