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* Copyright (c) 2012 The Broad Institute
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*
* The above copyright notice and this permission notice shall be
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package org.broadinstitute.gatk.tools.walkers.variantutils;
import org.broadinstitute.gatk.utils.BaseTest;
import org.broadinstitute.gatk.utils.Utils;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
public class SelectVariantsUnitTest extends BaseTest {
//////////////////////////////////////////
// Tests for maxIndelSize functionality //
//////////////////////////////////////////
@DataProvider(name = "MaxIndelSize")
public Object[][] MaxIndelSizeTestData() {
List<Object[]> tests = new ArrayList<Object[]>();
for ( final int size : Arrays.asList(1, 3, 10, 100) ) {
for ( final int otherSize : Arrays.asList(0, 1) ) {
for ( final int max : Arrays.asList(0, 1, 5, 50, 100000) ) {
for ( final String op : Arrays.asList("D", "I") ) {
tests.add(new Object[]{size, otherSize, max, op});
}
}
}
}
return tests.toArray(new Object[][]{});
}
@Test(dataProvider = "MaxIndelSize")
public void maxIndelSizeTest(final int size, final int otherSize, final int max, final String op) {
final byte[] largerAllele = Utils.dupBytes((byte) 'A', size+1);
final byte[] smallerAllele = Utils.dupBytes((byte) 'A', 1);
final List<Allele> alleles = new ArrayList<Allele>(2);
final Allele ref = Allele.create(op.equals("I") ? smallerAllele : largerAllele, true);
final Allele alt = Allele.create(op.equals("D") ? smallerAllele : largerAllele, false);
alleles.add(ref);
alleles.add(alt);
if ( otherSize > 0 && otherSize != size ) {
final Allele otherAlt = Allele.create(op.equals("D") ? Utils.dupBytes((byte) 'A', size-otherSize+1) : Utils.dupBytes((byte) 'A', otherSize+1), false);
alleles.add(otherAlt);
}
final VariantContext vc = new VariantContextBuilder("test", "1", 10, 10 + ref.length() - 1, alleles).make();
boolean hasTooLargeIndel = SelectVariants.containsIndelLargerThan(vc, max);
Assert.assertEquals(hasTooLargeIndel, size > max);
}
}