84 lines
2.7 KiB
Java
84 lines
2.7 KiB
Java
// our package
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package org.broadinstitute.sting.utils;
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// the imports for unit testing.
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import org.junit.Assert;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import org.broadinstitute.sting.BaseTest;
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import java.io.File;
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import java.io.FileNotFoundException;
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import net.sf.picard.reference.ReferenceSequenceFile;
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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/**
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* Basic unit test for GenomeLoc
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*/
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public class GenomeLocUnitTest extends BaseTest {
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private static ReferenceSequenceFile seq;
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@BeforeClass
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public static void init() throws FileNotFoundException {
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// sequence
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seq = new IndexedFastaSequenceFile(new File(hg18Reference));
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GenomeLocParser.setupRefContigOrdering(seq);
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}
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/**
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* Tests that we got a string parameter in correctly
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*/
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@Test
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public void testIsBetween() {
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logger.warn("Executing testIsBetween");
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GenomeLoc locMiddle = GenomeLocParser.createGenomeLoc("chr1", 3, 3);
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GenomeLoc locLeft = GenomeLocParser.createGenomeLoc("chr1", 1, 1);
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GenomeLoc locRight = GenomeLocParser.createGenomeLoc("chr1", 5, 5);
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Assert.assertTrue(locMiddle.isBetween(locLeft, locRight));
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Assert.assertFalse(locLeft.isBetween(locMiddle, locRight));
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Assert.assertFalse(locRight.isBetween(locLeft, locMiddle));
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}
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@Test
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public void testContigIndex() {
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logger.warn("Executing testContigIndex");
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GenomeLoc locOne = GenomeLocParser.createGenomeLoc("chr1",1,1);
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Assert.assertEquals(locOne.getContigIndex(), 1);
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Assert.assertEquals(locOne.getContig(), "chr1");
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GenomeLoc locX = GenomeLocParser.createGenomeLoc("chrX",1,1);
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Assert.assertEquals(locX.getContigIndex(), 23);
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Assert.assertEquals(locX.getContig(), "chrX");
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GenomeLoc locNumber = GenomeLocParser.createGenomeLoc(1,1,1);
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Assert.assertEquals(locNumber.getContigIndex(), 1);
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Assert.assertEquals(locNumber.getContig(), "chr1");
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Assert.assertEquals(locOne.compareTo(locNumber), 0);
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}
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@Test
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public void testCompareTo() {
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logger.warn("Executing testCompareTo");
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GenomeLoc twoOne = GenomeLocParser.createGenomeLoc("chr2", 1);
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GenomeLoc twoFive = GenomeLocParser.createGenomeLoc("chr2", 5);
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GenomeLoc twoOtherFive = GenomeLocParser.createGenomeLoc("chr2", 5);
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Assert.assertEquals(0, twoFive.compareTo(twoOtherFive));
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Assert.assertEquals(-1, twoOne.compareTo(twoFive));
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Assert.assertEquals(1, twoFive.compareTo(twoOne));
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GenomeLoc oneOne = GenomeLocParser.createGenomeLoc("chr1", 5);
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Assert.assertEquals(-1, oneOne.compareTo(twoOne));
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Assert.assertEquals(1, twoOne.compareTo(oneOne));
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}
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} |