/*******************************************************************************
* 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;
}
}