/*
* The MIT License
*
* 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 picard.vcf;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import htsjdk.variant.variantcontext.VariantContextComparator;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedHashSet;
import java.util.List;
public class VariantContextComparatorTest {
private static VariantContext buildVariantContext(final String source, final String contig, final long start) {
final Collection<Allele> alleles = new ArrayList<Allele>();
alleles.add(Allele.create("AAAA", true));
alleles.add(Allele.create("AAGG", false));
return new VariantContextBuilder(source, contig, start, start + 3, alleles).make();
}
private static List<String> getOrderedContigList(final VariantContext... variantContexts) {
final LinkedHashSet<String> contigs = new LinkedHashSet<String>();
for (final VariantContext context : variantContexts) {
contigs.add(context.getChr());
}
return new ArrayList<String>(contigs);
}
@Test
public void testIdentical() {
final VariantContext contextOne = buildVariantContext("source", "one", 100);
final List<String> contigs = getOrderedContigList(contextOne);
Assert.assertEquals(0, new VariantContextComparator(contigs).compare(contextOne, contextOne));
}
@Test
public void testPositions() {
final VariantContext contextOne = buildVariantContext("source", "one", 100);
final VariantContext contextTwo = buildVariantContext("source", "one", 150);
final List<String> contigs = getOrderedContigList(contextOne, contextTwo);
Assert.assertTrue(new VariantContextComparator(contigs).compare(contextOne, contextTwo) < 0);
Assert.assertTrue(new VariantContextComparator(contigs).compare(contextTwo, contextOne) > 0);
}
@Test
public void testContigs() {
final VariantContext contextOne = buildVariantContext("source", "one", 100);
final VariantContext contextTwo = buildVariantContext("source", "two", 100);
final List<String> contigs = getOrderedContigList(contextOne, contextTwo);
Assert.assertTrue(new VariantContextComparator(contigs).compare(contextOne, contextTwo) < 0);
Assert.assertTrue(new VariantContextComparator(contigs).compare(contextTwo, contextOne) > 0);
}
@Test
public void testCombinationOne() {
final VariantContext contextOne = buildVariantContext("source", "one", 100);
final VariantContext contextTwo = buildVariantContext("source", "two", 150);
final List<String> contigs = getOrderedContigList(contextOne, contextTwo);
Assert.assertTrue(new VariantContextComparator(contigs).compare(contextOne, contextTwo) < 0);
Assert.assertTrue(new VariantContextComparator(contigs).compare(contextTwo, contextOne) > 0);
}
@Test
public void testCombinationTwo() {
final VariantContext contextOne = buildVariantContext("source", "one", 150);
final VariantContext contextTwo = buildVariantContext("source", "two", 100);
final List<String> contigs = getOrderedContigList(contextOne, contextTwo);
Assert.assertTrue(new VariantContextComparator(contigs).compare(contextOne, contextTwo) < 0);
Assert.assertTrue(new VariantContextComparator(contigs).compare(contextTwo, contextOne) > 0);
}
@Test (expectedExceptions = IllegalArgumentException.class)
public void testThrowsOnDuplicateContig() {
final List<String> contigs = new ArrayList<String>(3);
contigs.add("one");
contigs.add("two");
contigs.add("one");
new VariantContextComparator(contigs);
}
}