/*
* Eoulsan development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public License version 2.1 or
* later and CeCILL-C. This should be distributed with the code.
* If you do not have a copy, see:
*
* http://www.gnu.org/licenses/lgpl-2.1.txt
* http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
*
* Copyright for this code is held jointly by the Genomic platform
* of the Institut de Biologie de l'École normale supérieure and
* the individual authors. These should be listed in @author doc
* comments.
*
* For more information on the Eoulsan project and its aims,
* or to join the Eoulsan Google group, visit the home page
* at:
*
* http://outils.genomique.biologie.ens.fr/eoulsan
*
*/
package fr.ens.biologie.genomique.eoulsan.bio.alignmentsfilters;
import htsjdk.samtools.SAMRecord;
import java.util.List;
/**
* This alignments filter remove all the alignments if more there is more one
* alignments for a read.
* @since 1.1
* @author Laurent Jourdren
* @author Claire Wallon
*/
public class RemoveMultiMatchesReadAlignmentsFilter
extends AbstractReadAlignmentsFilter {
public static final String FILTER_NAME = "removemultimatches";
@Override
public String getName() {
return FILTER_NAME;
}
@Override
public String getDescription() {
return "Remove all the alignments with several matches";
}
@Override
public void filterReadAlignments(final List<SAMRecord> records) {
if (records == null || records.isEmpty()) {
return;
}
// single-end mode
if (!records.get(0).getReadPairedFlag()) {
if (records.size() > 1) {
records.clear();
}
}
// paired-end mode
else {
switch (records.size()) {
case 1:
return;
case 2:
int countFirstInPair = 0;
int countSecondInPair = 0;
for (SAMRecord record : records) {
if (record.getFirstOfPairFlag()) {
countFirstInPair++;
} else if (record.getSecondOfPairFlag()) {
countSecondInPair++;
}
}
if (countFirstInPair > 1 || countSecondInPair > 1) {
records.clear();
}
break;
default:
records.clear();
break;
}
}
}
@Override
public String toString() {
return this.getClass().getSimpleName() + "{name=" + getName() + "}";
}
}