/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.engine.filters;
import htsjdk.samtools.SAMRecord;
import org.broadinstitute.gatk.engine.arguments.ValidationExclusion;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.util.Collections;
/**
* Tests for the {@link MalformedReadFilter} when the unsafe flag
* {@link ValidationExclusion.TYPE#ALLOW_N_CIGAR_READS} is set.
*
* @author Valentin Ruano-Rubio
* @since 6/6/13
*/
public class AllowNCigarMalformedReadFilterUnitTest extends MalformedReadFilterUnitTest {
@Override
protected ValidationExclusion composeValidationExclusion() {
return new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALLOW_N_CIGAR_READS));
}
@Test(enabled = true,
dataProvider= "UnsupportedCigarOperatorDataProvider")
@CigarOperatorTest(CigarOperatorTest.Outcome.IGNORE)
public void testCigarNOperatorFilterIgnore(final String cigarString) {
final MalformedReadFilter filter = buildMalformedReadFilter(false);
final SAMRecord nContainingCigarRead = buildSAMRecord(cigarString);
Assert.assertFalse(filter.filterOut(nContainingCigarRead),
"filters out N containing Cigar when it should ignore the fact");
}
@Test(enabled = false)
@Override
public void testCigarNOperatorFilterException(final String cigarString) {
// Nothing to do here.
// Just deactivates the parents test case.
}
}