/*
* 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.tools.walkers.readutils;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMRecord;
import org.broadinstitute.gatk.utils.BaseTest;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.utils.sam.ArtificialReadsTraversal;
import org.broadinstitute.gatk.utils.sam.ArtificialGATKSAMFileWriter;
import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
/*
* Copyright (c) 2009 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.
*/
/**
* @author aaron
* <p/>
* Class PrintReadsUnitTest
* <p/>
* This tests the print reads walker, using the artificial reads traversal
*/
public class PrintReadsUnitTest extends BaseTest {
/**
* our private fake reads traversal. This traversal seeds the
* the walker with a specified number of fake reads, which are named sequentially
*/
private ArtificialReadsTraversal trav;
private int readTotal = 0;
//private char bases[] = {'a', 't'};
private ReferenceContext bases = null;
//private ReferenceContext ref = new ReferenceContext()
org.broadinstitute.gatk.tools.walkers.readutils.PrintReads walker;
ArtificialGATKSAMFileWriter writer;
@BeforeMethod
public void before() {
trav = new ArtificialReadsTraversal();
readTotal = ( ( trav.endingChr - trav.startingChr ) + 1 ) * trav.readsPerChr + trav.unMappedReads;
walker = new org.broadinstitute.gatk.tools.walkers.readutils.PrintReads();
writer = new ArtificialGATKSAMFileWriter();
walker.initialize();
}
/** test that we get out the same number of reads we put in */
@Test
public void testReadCount() {
trav.traverse(walker, null, writer);
assertEquals(writer.getRecords().size(), readTotal);
}
/** test that we're ok with a null read */
@Test
public void testNullRead() {
SAMRecord rec = walker.map(bases, null, null);
assertTrue(rec == null);
}
/** tes that we get the read we put into the map function */
@Test
public void testReturnRead() {
SAMFileHeader head = ArtificialSAMUtils.createArtificialSamHeader(3,1,1000);
GATKSAMRecord rec = ArtificialSAMUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
SAMRecord ret = walker.map(bases, rec, null);
assertTrue(ret == rec);
assertTrue(ret.getReadName().equals(rec.getReadName()));
}
}