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Fixed broken VariantEval stratifications VariantType and IndelSize - integration tests to follow

This commit is contained in:
Guillermo del Angel 2012-06-03 08:38:38 -04:00
parent 4bc04e2a9e
commit 2ddbdee3bc
2 changed files with 8 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java
View File

@ -47,4 +47,8 @@ public class IndelSize extends VariantStratifier {
return Collections.emptyList(); return Collections.emptyList();
} }
@Override
public String getFormat() {
return "%d";
}
} }

6
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
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@ -38,10 +38,12 @@ import java.util.List;
public class VariantType extends VariantStratifier { public class VariantType extends VariantStratifier {
@Override @Override
public void initialize() { public void initialize() {
states.addAll(Arrays.asList(VariantContext.Type.values())); for (VariantContext.Type t : VariantContext.Type.values())
states.add(t.toString());
} }
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
return eval == null ? Collections.emptyList() : Collections.singletonList((Object)eval.getType()); return eval == null ? Collections.emptyList() : Collections.singletonList((Object)eval.getType().toString());
} }
} }