/*
 * The Exomiser - A tool to annotate and prioritize genomic variants
 *
 * Copyright (c) 2016-2019 Queen Mary University of London.
 * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package org.monarchinitiative.exomiser.core.genome.dao;

import htsjdk.tribble.readers.TabixReader;

import java.io.Closeable;

/**
 * Abstraction for querying Tabix files. The HTSJK TabixReader is not easy to test and provides no interface or
 * alternate implementations. This partially mitigates this issue as the Tabix.Iterator does not implement
 * java.util.Iterator.
 *
 * @author Jules Jacobsen <j.jacobsen@qmul.ac.uk>
 */
public interface TabixDataSource extends Closeable {

    public TabixReader.Iterator query(String query);

    public TabixReader.Iterator query(String chromosome, int start, int end);

    public String getSource();

}
/*
 * The Exomiser - A tool to annotate and prioritize genomic variants
 *
 * Copyright (c) 2016-2020 Queen Mary University of London.
 * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package org.monarchinitiative.exomiser.core.genome.dao;

import htsjdk.tribble.readers.TabixReader;

import java.io.Closeable;

/**
 * Abstraction for querying Tabix files. The HTSJK TabixReader is not easy to test and provides no interface or
 * alternate implementations. This partially mitigates this issue as the Tabix.Iterator does not implement
 * java.util.Iterator.
 *
 * @author Jules Jacobsen <j.jacobsen@qmul.ac.uk>
 */
public interface TabixDataSource extends Closeable {

    TabixReader.Iterator query(String query);

    TabixReader.Iterator query(String chromosome, int start, int end);

    String getSource();

}
Update TabixDataSource to remove redundant public keywords