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Don't cast to a specific walker type since any walker can use the VA engine

This commit is contained in:
Eric Banks 2012-07-09 10:23:26 -04:00
parent 5b0ade67c8
commit dd0c47ab7e
1 changed files with 2 additions and 1 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
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@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.gatk.samples.SampleDB;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
@ -33,7 +34,7 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( mendelianViolation == null ) {
if (checkAndSetSamples(((VariantAnnotator) walker).getSampleDB())) {
if (checkAndSetSamples(((Walker) walker).getSampleDB())) {
mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).minGenotypeQualityP );
}
else {