/*
* 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.readsfilters;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import org.junit.Test;
import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import fr.ens.biologie.genomique.eoulsan.bio.ReadSequence;
import fr.ens.biologie.genomique.eoulsan.bio.readsfilters.ReadFilter;
import fr.ens.biologie.genomique.eoulsan.bio.readsfilters.ReadNameStartsWithReadFilter;
public class ReadNameStartsWithReadFilterTest {
@Test
public void testAcceptReadSequence() throws EoulsanException {
ReadFilter filter = new ReadNameStartsWithReadFilter();
filter.setParameter("allowed.prefixes", "AEGIR");
filter.init();
// Null case
assertFalse(filter.accept(null));
final String[] ids = {"AEGIR:25:B0866ABXX:8:1101:1193:2125",
"TOTO:25:B0866ABXX:8:1101:1176:2126",
"TOTO:25:B0866ABXX:8:1102:1111:4444",
"TOTO:25:B0866ABXX:8:1202:5555:6666",
"TOTO:25:B0866ABXX:7:2202:1176:2126",
"TOTO:25:B0866ABXX:8:1301:2222:3333"};
// Not illumina id case
ReadSequence read = new ReadSequence(0, "read1", "ATG", "wxy");
assertFalse(filter.accept(read));
assertTrue(filter.accept(new ReadSequence(0, ids[0], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[1], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[2], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[3], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[4], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[5], "", "")));
filter = new ReadNameStartsWithReadFilter();
filter.setParameter("allowed.prefixes",
"TOTO:25:B0866ABXX:8:11, " + "TOTO:25:B0866ABXX:8:13");
filter.init();
assertFalse(filter.accept(new ReadSequence(0, ids[0], "", "")));
assertTrue(filter.accept(new ReadSequence(0, ids[1], "", "")));
assertTrue(filter.accept(new ReadSequence(0, ids[2], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[3], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[4], "", "")));
assertTrue(filter.accept(new ReadSequence(0, ids[5], "", "")));
filter = new ReadNameStartsWithReadFilter();
filter.setParameter("forbidden.prefixes",
"TOTO:25:B0866ABXX:8:11, " + "TOTO:25:B0866ABXX:8:13");
filter.init();
assertTrue(filter.accept(new ReadSequence(0, ids[0], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[1], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[2], "", "")));
assertTrue(filter.accept(new ReadSequence(0, ids[3], "", "")));
assertTrue(filter.accept(new ReadSequence(0, ids[4], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[5], "", "")));
filter = new ReadNameStartsWithReadFilter();
filter.setParameter("allowed.prefixes", "TOTO");
filter.setParameter("forbidden.prefixes",
"TOTO:25:B0866ABXX:8:11, " + "TOTO:25:B0866ABXX:8:13");
filter.init();
assertFalse(filter.accept(new ReadSequence(0, ids[0], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[1], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[2], "", "")));
assertTrue(filter.accept(new ReadSequence(0, ids[3], "", "")));
assertTrue(filter.accept(new ReadSequence(0, ids[4], "", "")));
assertFalse(filter.accept(new ReadSequence(0, ids[5], "", "")));
}
}