/*
* Copyright (c) 2012 The Broad Institute
*
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* obtaining a copy of this software and associated documentation
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* 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,
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package org.broadinstitute.gatk.utils.sam;
import org.broadinstitute.gatk.utils.BaseTest;
import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import static org.testng.Assert.fail;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMRecord;
/**
* Created by IntelliJ IDEA.
* User: aaronmckenna
* Date: Jun 3, 2009
* Time: 3:09:34 AM
* To change this template use File | Settings | File Templates.
*/
public class ArtificialSAMUtilsUnitTest extends BaseTest {
@Test
public void basicReadIteratorTest() {
GATKSAMIterator iter = ArtificialSAMUtils.mappedReadIterator(1, 100, 100);
int count = 0;
while (iter.hasNext()) {
SAMRecord rec = iter.next();
count++;
}
assertEquals(count, 100 * 100);
}
@Test
public void tenPerChromosome() {
GATKSAMIterator iter = ArtificialSAMUtils.mappedReadIterator(1, 100, 10);
int count = 0;
while (iter.hasNext()) {
SAMRecord rec = iter.next();
assertEquals(Integer.valueOf(Math.round(count / 10)), rec.getReferenceIndex());
count++;
}
assertEquals(count, 100 * 10);
}
@Test
public void onePerChromosome() {
GATKSAMIterator iter = ArtificialSAMUtils.mappedReadIterator(1, 100, 1);
int count = 0;
while (iter.hasNext()) {
SAMRecord rec = iter.next();
assertEquals(Integer.valueOf(count), rec.getReferenceIndex());
count++;
}
assertEquals(count, 100 * 1);
}
@Test
public void basicUnmappedIteratorTest() {
GATKSAMIterator iter = ArtificialSAMUtils.mappedAndUnmappedReadIterator(1, 100, 100, 1000);
int count = 0;
for (int x = 0; x < (100* 100); x++ ) {
if (!iter.hasNext()) {
fail ("we didn't get the expected number of reads");
}
SAMRecord rec = iter.next();
assertTrue(rec.getReferenceIndex() >= 0);
count++;
}
assertEquals(100 * 100, count);
// now we should have 1000 unmapped reads
count = 0;
while (iter.hasNext()) {
SAMRecord rec = iter.next();
assertTrue(rec.getReferenceIndex() < 0);
count++;
}
assertEquals(count, 1000);
}
}