77 lines
2.3 KiB
Java
77 lines
2.3 KiB
Java
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// 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.*;
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import static org.junit.Assert.*;
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import org.apache.commons.cli.ParseException;
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import org.broadinstitute.sting.utils.cmdLine.ArgumentParser;
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import java.util.ArrayList;
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import java.io.File;
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/**
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* Basic unit test for GenomeLoc
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*/
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public class GenomeLocTest {
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private static FastaSequenceFile2 seq;
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@BeforeClass
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public static void init() {
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// sequence
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seq = new FastaSequenceFile2(new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
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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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GenomeLoc.setupRefContigOrdering(seq);
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GenomeLoc locMiddle = new GenomeLoc("chr1", 3, 3);
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GenomeLoc locLeft = new GenomeLoc("chr1", 1, 1);
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GenomeLoc locRight = new GenomeLoc("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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GenomeLoc locOne = new GenomeLoc("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 = new GenomeLoc("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 = new GenomeLoc(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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GenomeLoc twoOne = new GenomeLoc("chr2", 1);
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GenomeLoc twoFive = new GenomeLoc("chr2", 5);
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GenomeLoc twoOtherFive = new GenomeLoc("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 = new GenomeLoc("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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}
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