/*
* Copyright (c) 2012 The Broad Institute
*
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* obtaining a copy of this software and associated documentation
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* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
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*
* The above copyright notice and this permission notice shall be
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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package org.broadinstitute.gatk.engine.traversals;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMRecord;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.testng.Assert;
import org.broadinstitute.gatk.utils.BaseTest;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
/**
* @author aaron
* <p/>
* Class TraverseDuplicatesUnitTest
* <p/>
* test the meat of the traverse dupplicates.
*/
public class TraverseDuplicatesUnitTest extends BaseTest {
private TraverseDuplicates obj = new TraverseDuplicates();
private SAMFileHeader header;
private GenomeLocParser genomeLocParser;
private GenomeAnalysisEngine engine;
private File refFile = new File(validationDataLocation + "Homo_sapiens_assembly17.fasta");
@BeforeMethod
public void doBefore() {
header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
genomeLocParser =new GenomeLocParser(header.getSequenceDictionary());
engine = new GenomeAnalysisEngine();
engine.setReferenceDataSource(refFile);
engine.setGenomeLocParser(genomeLocParser);
obj.initialize(engine, null);
}
@Test
public void testAllDuplicatesNoPairs() {
List<SAMRecord> list = new ArrayList<SAMRecord>();
for (int x = 0; x < 10; x++) {
SAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "SWEET_READ" + x, 0, 1, 100);
read.setDuplicateReadFlag(true);
list.add(read);
}
Set<List<SAMRecord>> myPairings = obj.uniqueReadSets(list);
Assert.assertEquals(myPairings.size(), 1);
Assert.assertEquals(myPairings.iterator().next().size(), 10); // dup's
}
@Test
public void testNoDuplicatesNoPairs() {
List<SAMRecord> list = new ArrayList<SAMRecord>();
for (int x = 0; x < 10; x++) {
SAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "SWEET_READ" + x, 0, 1, 100);
read.setDuplicateReadFlag(false);
list.add(read);
}
Set<List<SAMRecord>> myPairing = obj.uniqueReadSets(list);
Assert.assertEquals(myPairing.size(), 10); // unique
}
@Test
public void testFiftyFiftyNoPairs() {
List<SAMRecord> list = new ArrayList<SAMRecord>();
for (int x = 0; x < 5; x++) {
SAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "SWEET_READ" + x, 0, 1, 100);
read.setDuplicateReadFlag(true);
list.add(read);
}
for (int x = 10; x < 15; x++)
list.add(ArtificialSAMUtils.createArtificialRead(header, String.valueOf(x), 0, x, 100));
Set<List<SAMRecord>> myPairing = obj.uniqueReadSets(list);
Assert.assertEquals(myPairing.size(), 6); // unique
}
@Test
public void testAllDuplicatesAllPairs() {
List<SAMRecord> list = new ArrayList<SAMRecord>();
for (int x = 0; x < 10; x++) {
SAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "SWEET_READ"+ x, 0, 1, 100);
read.setDuplicateReadFlag(true);
read.setMateAlignmentStart(100);
read.setMateReferenceIndex(0);
read.setReadPairedFlag(true);
list.add(read);
}
Set<List<SAMRecord>> myPairing = obj.uniqueReadSets(list);
Assert.assertEquals(myPairing.size(), 1); // unique
}
@Test
public void testNoDuplicatesAllPairs() {
List<SAMRecord> list = new ArrayList<SAMRecord>();
for (int x = 0; x < 10; x++) {
SAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "SWEET_READ"+ x, 0, 1, 100);
if (x == 0) read.setDuplicateReadFlag(true); // one is a dup but (next line)
read.setMateAlignmentStart(100); // they all have a shared start and mate start so they're dup's
read.setMateReferenceIndex(0);
read.setReadPairedFlag(true);
list.add(read);
}
Set<List<SAMRecord>> myPairing = obj.uniqueReadSets(list);
Assert.assertEquals(myPairing.size(), 1); // unique
}
@Test
public void testAllDuplicatesAllPairsDifferentPairedEnd() {
List<SAMRecord> list = new ArrayList<SAMRecord>();
for (int x = 0; x < 10; x++) {
SAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "SWEET_READ" + x, 0, 1, 100);
if (x == 0) read.setDuplicateReadFlag(true); // one is a dup
read.setMateAlignmentStart(100 + x);
read.setMateReferenceIndex(0);
read.setReadPairedFlag(true);
list.add(read);
}
Set<List<SAMRecord>> myPairing = obj.uniqueReadSets(list);
Assert.assertEquals(myPairing.size(), 10); // unique
}
}