28 lines
852 B
Java
28 lines
852 B
Java
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package org.broadinstitute.sting.alignment;
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import org.testng.annotations.Test;
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import org.broadinstitute.sting.WalkerTest;
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import java.util.Arrays;
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/**
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* Integration tests for the aligner.
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*
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* @author mhanna
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* @version 0.1
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*/
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public class AlignerIntegrationTest extends WalkerTest {
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@Test
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public void testBasicAlignment() {
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String md5 = "34eb4323742999d6d250a0aaa803c6d5";
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-R " + GATKDataLocation + "bwa/human_b36_both.fasta" +
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" -T Align" +
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" -I " + validationDataLocation + "NA12878_Pilot1_20.trimmed.unmapped.bam" +
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" -o %s",
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1, // just one output file
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Arrays.asList(md5));
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executeTest("testBasicAlignment", spec);
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}
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}
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