44 lines
1.5 KiB
Java
44 lines
1.5 KiB
Java
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package org.broadinstitute.sting.gatk;
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import net.sf.samtools.SAMFileReader;
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import org.broadinstitute.sting.BaseTest;
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import org.testng.Assert;
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import org.testng.annotations.Test;
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import java.io.File;
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/**
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* @author Eric Banks
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* @since 7/18/12
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*/
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public class CommandLineGATKUnitTest extends BaseTest {
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@Test(enabled = true)
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public void testSamTextFileError1() {
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final File samFile = new File(publicTestDir + "testfile.sam");
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final File indexFile = new File(publicTestDir + "HiSeq.1mb.1RG.bai");
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try {
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final SAMFileReader reader = new SAMFileReader(samFile, indexFile, false);
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// we shouldn't get here
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Assert.fail("We should have exceptioned out when trying to create a reader with an index for a textual SAM file");
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} catch (RuntimeException e) {
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Assert.assertTrue(e.getMessage().indexOf(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_1) != -1);
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}
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}
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@Test(enabled = true)
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public void testSamTextFileError2() {
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File samFile = new File(publicTestDir + "testfile.sam");
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try {
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final SAMFileReader reader = new SAMFileReader(samFile);
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reader.getFilePointerSpanningReads();
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// we shouldn't get here
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Assert.fail("We should have exceptioned out when trying to call getFilePointerSpanningReads() for a textual SAM file");
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} catch (RuntimeException e) {
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Assert.assertTrue(e.getMessage().indexOf(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_2) != -1);
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}
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}
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}
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