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Bug fix for strict validation: rsID checking wasn't working if there were multiple IDs

This commit is contained in:
Eric Banks 2012-12-17 10:32:41 -05:00
parent 1d18ee26cc
commit 762f184262
1 changed files with 3 additions and 1 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
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@ -34,12 +34,14 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File; import java.io.File;
import java.util.Arrays;
import java.util.Collection; import java.util.Collection;
import java.util.HashSet; import java.util.HashSet;
import java.util.Set; import java.util.Set;
@ -149,7 +151,7 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
if ( tracker.hasValues(dbsnp.dbsnp) ) { if ( tracker.hasValues(dbsnp.dbsnp) ) {
rsIDs = new HashSet<String>(); rsIDs = new HashSet<String>();
for ( VariantContext rsID : tracker.getValues(dbsnp.dbsnp, ref.getLocus()) ) for ( VariantContext rsID : tracker.getValues(dbsnp.dbsnp, ref.getLocus()) )
rsIDs.add(rsID.getID()); rsIDs.addAll(Arrays.asList(rsID.getID().split(VCFConstants.ID_FIELD_SEPARATOR)));
} }
try { try {