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Fix in AnalyzeAnnotations, somebody changed it look for ID in the vc's info field. This dinosaur desperately needs integration tests. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4338 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-09-23 19:48:44 +00:00
parent 0c781968fb
commit 0c9fabb06f
1 changed files with 3 additions and 2 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.analyzeannotations; package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
@ -85,11 +86,11 @@ public class AnnotationDataManager {
treeSet.add(datum); treeSet.add(datum);
} }
final boolean isNovelVariant = infoField.containsKey(VariantContext.ID_KEY); final boolean isNovelVariant = !infoField.get(VariantContext.ID_KEY).toString().contains("rs");
// Decide if the variant is a transition or transversion // Decide if the variant is a transition or transversion
if ( vc.isSNP() ) { if ( vc.isSNP() ) {
if( BaseUtils.isTransition( vc.getReference().getBases()[0], vc.getAlternateAllele(0).getBases()[0]) ) { if( VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0 ) {
datum.incrementTi( isNovelVariant, isInTruthSet, isTrueVariant ); datum.incrementTi( isNovelVariant, isInTruthSet, isTrueVariant );
} else { } else {
datum.incrementTv( isNovelVariant, isInTruthSet, isTrueVariant ); datum.incrementTv( isNovelVariant, isInTruthSet, isTrueVariant );