/*
* 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.utils.sam;
import org.broadinstitute.gatk.utils.BaseTest;
import static org.testng.Assert.assertTrue;
import static org.testng.Assert.fail;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMRecord;
/*
* 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
*
* Class ArtificialPatternedSAMIteratorUnitTest
*
* tests ArtificialPatternedSAMIterator, making sure that if you specify in order
* you get reads in order, and if you specify out of order you get them out of order.
*/
public class ArtificialPatternedSAMIteratorUnitTest extends BaseTest {
// our artifical patterned iterator
ArtificialPatternedSAMIterator iter;
private int startingChr = 1;
private int endingChr = 2;
private int readCount = 100;
private int DEFAULT_READ_LENGTH = ArtificialSAMUtils.DEFAULT_READ_LENGTH;
SAMFileHeader header;
@BeforeMethod
public void before() {
header = ArtificialSAMUtils.createArtificialSamHeader(( endingChr - startingChr ) + 1, startingChr, readCount + DEFAULT_READ_LENGTH);
}
@Test
public void testInOrder() {
iter = new ArtificialPatternedSAMIterator(startingChr,endingChr,readCount,0,header, ArtificialPatternedSAMIterator.PATTERN.IN_ORDER_READS);
if (!iter.hasNext()) {
fail("no reads in the ArtificialPatternedSAMIterator");
}
SAMRecord last = iter.next();
while (iter.hasNext()) {
SAMRecord rec = iter.next();
if (!(rec.getReferenceIndex() > last.getReferenceIndex()) && (rec.getAlignmentStart() <= last.getAlignmentStart())) {
fail("read " + rec.getReadName() + " out of order compared to last read, " + last.getReadName());
}
last = rec;
}
}
@Test
public void testOutOfOrder() {
int outOfOrderCount = 0;
iter = new ArtificialPatternedSAMIterator(startingChr,endingChr,readCount,0,header, ArtificialPatternedSAMIterator.PATTERN.RANDOM_READS);
if (!iter.hasNext()) {
fail("no reads in the ArtificialPatternedSAMIterator");
}
SAMRecord last = iter.next();
while (iter.hasNext()) {
SAMRecord rec = iter.next();
if (!(rec.getReferenceIndex() > last.getReferenceIndex()) && (rec.getAlignmentStart() <= last.getAlignmentStart())) {
++outOfOrderCount;
}
last = rec;
}
assertTrue(outOfOrderCount > 0);
}
}