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Adding function call in HaplotypeCaller right before the VariantContext gets written out to disk which partitions all the reads by which allele gave the read the highest likelihood. This will allow variants to be annotated by the refactored VariantAnnotator. Uninformative reads are mapped to Allele.NO_CALL

This commit is contained in:
Ryan Poplin 2012-04-06 00:22:52 -04:00
parent a19c27297f
commit c77104b815
1 changed files with 10 additions and 2 deletions
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12
public/java/src/org/broadinstitute/sting/utils/Haplotype.java
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@ -27,12 +27,11 @@ package org.broadinstitute.sting.utils;
import com.google.java.contract.Ensures; import com.google.java.contract.Ensures;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import net.sf.samtools.Cigar; 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.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*; import java.util.*;
@ -41,6 +40,7 @@ public class Haplotype {
protected final double[] quals; protected final double[] quals;
private GenomeLoc genomeLocation = null; private GenomeLoc genomeLocation = null;
private HashMap<String, double[]> readLikelihoodsPerSample = null; private HashMap<String, double[]> readLikelihoodsPerSample = null;
private HashMap<Integer, VariantContext> eventMap = null;
private boolean isRef = false; private boolean isRef = false;
private Cigar cigar; private Cigar cigar;
private int alignmentStartHapwrtRef; private int alignmentStartHapwrtRef;
@ -97,6 +97,14 @@ public class Haplotype {
return readLikelihoodsPerSample.keySet(); return readLikelihoodsPerSample.keySet();
} }
public HashMap<Integer, VariantContext> getEventMap() {
return eventMap;
}
public void setEventMap( final HashMap<Integer, VariantContext> eventMap ) {
this.eventMap = eventMap;
}
public boolean isReference() { public boolean isReference() {
return isRef; return isRef;
} }