/*******************************************************************************
* 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.IO.utils.SAMRecordFilter;
import net.sf.samtools.SAMRecord;
/**
* Filters out {@link SAMRecord} that are not uniquely aligned and that are not primary alignments
* @author Julien Lajugie
*/
public class NotUniqueNorPrimarySAMRecordFilter implements SAMRecordFilter {
@Override
public SAMRecord applyFilter(SAMRecord samRecord) {
String typeBWAFlag = (String) samRecord.getAttribute("XT");
if (samRecord.getNotPrimaryAlignmentFlag()) {
return ((typeBWAFlag != null) && typeBWAFlag.equalsIgnoreCase("U")) ? samRecord : null;
} else {
return samRecord;
}
}
}