88 lines
2.9 KiB
Java
88 lines
2.9 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.testng.Assert;
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import org.testng.annotations.BeforeClass;
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import org.testng.annotations.Test;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
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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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private GenomeLocParser genomeLocParser;
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@BeforeClass
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public void init() throws FileNotFoundException {
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// sequence
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seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
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genomeLocParser = new GenomeLocParser(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(1, locOne.getContigIndex());
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Assert.assertEquals("chr1", locOne.getContig());
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GenomeLoc locX = genomeLocParser.createGenomeLoc("chrX",1,1);
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Assert.assertEquals(23, locX.getContigIndex());
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Assert.assertEquals("chrX", locX.getContig());
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GenomeLoc locNumber = genomeLocParser.createGenomeLoc(seq.getSequenceDictionary().getSequence(1).getSequenceName(),1,1);
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Assert.assertEquals(1, locNumber.getContigIndex());
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Assert.assertEquals("chr1", locNumber.getContig());
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Assert.assertEquals(0, locOne.compareTo(locNumber));
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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(twoFive.compareTo(twoOtherFive), 0);
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Assert.assertEquals(twoOne.compareTo(twoFive), -1);
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Assert.assertEquals(twoFive.compareTo(twoOne), 1);
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GenomeLoc oneOne = genomeLocParser.createGenomeLoc("chr1", 5);
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Assert.assertEquals(oneOne.compareTo(twoOne), -1);
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Assert.assertEquals(twoOne.compareTo(oneOne), 1);
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}
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}
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