60 lines
2.1 KiB
Java
60 lines
2.1 KiB
Java
package org.broadinstitute.sting.utils.bed;
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import org.broadinstitute.sting.utils.GenomeLocParserTestUtils;
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import org.testng.Assert;
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import org.broadinstitute.sting.BaseTest;
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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.testng.annotations.BeforeClass;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.util.List;
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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public class BedParserUnitTest 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 void beforeTests() {
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GenomeLocParserTestUtils.clearSequenceDictionary();
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seq = new IndexedFastaSequenceFile(new File(b36KGReference));
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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(location.size(), 4);
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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(location.size(), 4);
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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(location.get(0).getStart(), 1);
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Assert.assertEquals(location.get(1).getStart(), 1002);
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Assert.assertEquals(location.get(2).getStart(), 1001);
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Assert.assertEquals(location.get(3).getStart(), 2001);
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// now check the the stop positions
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Assert.assertEquals(location.get(0).getStop(), 999);
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Assert.assertEquals(location.get(1).getStop(), 2000);
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Assert.assertEquals(location.get(2).getStop(), 5000);
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Assert.assertEquals(location.get(3).getStop(), 6000);
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}
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}
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