/*
* 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.ArrayList;
import java.util.List;
import fr.ens.biologie.genomique.eoulsan.EoulsanException;
/**
* This alignments filter keep a given number of the first alignments for a
* read.
* @since 1.2
* @author Claire Wallon
*/
public class KeepNumberMatchReadAlignmentsFilter
extends AbstractReadAlignmentsFilter {
public static final String FILTER_NAME = "keepnumbermatch";
private int numberMatch = -1;
@Override
public String getName() {
return FILTER_NAME;
}
@Override
public String getDescription() {
return "This filter allows to keep a given number of alignments of a read.";
}
@Override
public void setParameter(final String key, final String value)
throws EoulsanException {
if (key == null || value == null) {
return;
}
if ("threshold".equals(key.trim())) {
try {
this.numberMatch = Integer.parseInt(value.trim());
} catch (NumberFormatException e) {
return;
}
if (this.numberMatch < 0) {
throw new EoulsanException(
"Invalid number of match to keep: " + this.numberMatch);
}
} else {
throw new EoulsanException(
"Unknown parameter for " + getName() + " alignments filter: " + key);
}
}
@Override
public void init() {
if (this.numberMatch < 0) {
throw new IllegalArgumentException(
"The number of match to keep is not set for "
+ getName() + " alignments filter.");
}
}
@Override
public void filterReadAlignments(final List<SAMRecord> records) {
if (records == null || records.isEmpty()) {
return;
}
List<SAMRecord> recordsToKeep = new ArrayList<>();
int cptRecords = 0;
int nbRecordsToKeep;
// single-end mode
if (!records.get(0).getReadPairedFlag()) {
nbRecordsToKeep = this.numberMatch;
}
// paired-end mode
else {
nbRecordsToKeep = this.numberMatch * 2;
}
if (records.size() > nbRecordsToKeep) {
while (cptRecords < nbRecordsToKeep) {
recordsToKeep.add(records.get(cptRecords));
cptRecords++;
}
records.clear();
records.addAll(recordsToKeep);
}
}
@Override
public String toString() {
return this.getClass().getSimpleName()
+ "{name=" + getName() + ", numberMatch=" + this.numberMatch + "}";
}
}