MGOTBIIndex.java

/*******************************************************************************
 * GenPlay, Einstein Genome Analyzer
 * Copyright (C) 2009, 2014 Albert Einstein College of Medicine
 * 
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU 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 General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 * Authors: Julien Lajugie <julien.lajugie@einstein.yu.edu>
 *          Nicolas Fourel <nicolas.fourel@einstein.yu.edu>
 *          Eric Bouhassira <eric.bouhassira@einstein.yu.edu>
 * 
 * Website: <http://genplay.einstein.yu.edu>
 ******************************************************************************/
package edu.yu.einstein.genplay.core.multiGenome.operation.convert;

import java.io.File;

import net.sf.jannot.tabix.TabixConfiguration;
import net.sf.jannot.tabix.TabixWriter;
import edu.yu.einstein.genplay.util.Utils;


/**
 * @author Nicolas Fourel
 */
public class MGOTBIIndex {

	private final File bgzFile;	// the bgzip file
	private File tbiFile;		// the tbi file


	/**
	 * Constructor of {@link MGOTBIIndex}
	 * @param file the BGZIP file
	 */
	public MGOTBIIndex(File file) {
		bgzFile = file;
	}


	/**
	 * Index a BGZIP file using Tabix
	 * @return true if the operation has been done correctly. False otherwise.
	 * @throws Exception
	 */
	public Boolean compute() throws Exception {
		if (Utils.getExtension(bgzFile).equals("gz")) {
			tbiFile = new File(bgzFile.getPath() + ".tbi");
			tbiFile.createNewFile();
			TabixWriter writer = new TabixWriter(bgzFile, TabixConfiguration.VCF_CONF);
			writer.createIndex(tbiFile);
			return true;
		} else {
			return false;
		}
	}


	/**
	 * @return the tbiFile
	 */
	public File getTbiFile() {
		return tbiFile;
	}

}