76 lines
2.7 KiB
Java
76 lines
2.7 KiB
Java
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package org.broadinstitute.sting.utils.bed;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import org.junit.Assert;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* Created by IntelliJ IDEA.
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* User: aaron
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* Date: Oct 5, 2009
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* Time: 9:09:42 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class BedParserTest extends BaseTest {
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private static IndexedFastaSequenceFile seq;
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private File bedFile = new File("testdata/sampleBedFile.bed");
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@BeforeClass
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public static void beforeTests() {
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try {
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seq = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta"));
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} catch (FileNotFoundException e) {
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throw new StingException("unable to load the sequence dictionary");
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}
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GenomeLocParser.setupRefContigOrdering(seq);
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}
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@Test
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public void testLoadBedFile() {
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BedParser parser = new BedParser(bedFile);
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List<GenomeLoc> location = parser.getLocations();
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Assert.assertEquals(4, location.size());
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}
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@Test
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public void testBedParsing() {
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BedParser parser = new BedParser(bedFile);
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List<GenomeLoc> location = parser.getLocations();
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Assert.assertEquals(4, location.size());
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Assert.assertTrue(location.get(0).getContig().equals("20"));
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Assert.assertTrue(location.get(1).getContig().equals("20"));
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Assert.assertTrue(location.get(2).getContig().equals("22"));
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Assert.assertTrue(location.get(3).getContig().equals("22"));
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// now check the the start positions
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Assert.assertEquals(1, location.get(0).getStart());
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Assert.assertEquals(1002, location.get(1).getStart());
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Assert.assertEquals(1001, location.get(2).getStart());
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Assert.assertEquals(2001, location.get(3).getStart());
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// now check the the stop positions
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Assert.assertEquals(999, location.get(0).getStop());
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Assert.assertEquals(2000, location.get(1).getStop());
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Assert.assertEquals(5000, location.get(2).getStop());
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Assert.assertEquals(6000, location.get(3).getStop());
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}
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@Test
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public void testLoadBedFileOverlapping() {
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BedParser parser = new BedParser(bedFile);
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List<GenomeLoc> location = parser.getSortedAndMergedLocations();
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Assert.assertEquals(3, location.size());
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}
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}
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