HadoopDefaultVariantAnnotationManager.java

package org.opencb.opencga.storage.hadoop.variant.annotation;

import org.opencb.commons.datastore.core.QueryOptions;
import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor;
import org.opencb.opencga.storage.core.variant.annotation.DefaultVariantAnnotationManager;
import org.opencb.opencga.storage.core.variant.annotation.annotators.VariantAnnotator;
import org.opencb.opencga.storage.core.variant.io.db.VariantAnnotationDBWriter;
import org.opencb.opencga.storage.hadoop.variant.adaptors.VariantHadoopDBAdaptor;

/**
 * Created on 23/11/16.
 *
 * @author Jacobo Coll <jacobo167@gmail.com>
 */
public class HadoopDefaultVariantAnnotationManager extends DefaultVariantAnnotationManager {

    public HadoopDefaultVariantAnnotationManager(VariantAnnotator variantAnnotator, VariantDBAdaptor dbAdaptor) {
        super(variantAnnotator, dbAdaptor);
    }

    @Override
    protected VariantAnnotationDBWriter newVariantAnnotationDBWriter(VariantDBAdaptor dbAdaptor, QueryOptions options) {
        VariantHadoopDBAdaptor hadoopDBAdaptor = (VariantHadoopDBAdaptor) dbAdaptor;
        return hadoopDBAdaptor.newAnnotationLoader(options);
    }
}