org.broadinstitute.hellbender.engine.spark.VariantWalkerContext Maven / Gradle / Ivy
package org.broadinstitute.hellbender.engine.spark;
import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.hellbender.engine.FeatureContext;
import org.broadinstitute.hellbender.engine.ReadsContext;
import org.broadinstitute.hellbender.engine.ReferenceContext;
/**
* Encapsulates a {@link VariantContext} with the reads that overlap it (the {@link ReadsContext} and
* its {@link ReferenceContext} and {@link FeatureContext}.
*/
public class VariantWalkerContext {
private final VariantContext variant;
private final ReadsContext readsContext;
private final ReferenceContext referenceContext;
private final FeatureContext featureContext;
public VariantWalkerContext(VariantContext variant, ReadsContext readsContext, ReferenceContext referenceContext, FeatureContext featureContext) {
this.variant = variant;
this.readsContext = readsContext;
this.referenceContext = referenceContext;
this.featureContext = featureContext;
}
public VariantContext getVariant() {
return variant;
}
public ReadsContext getReadsContext() {
return readsContext;
}
public ReferenceContext getReferenceContext() {
return referenceContext;
}
public FeatureContext getFeatureContext() {
return featureContext;
}
}