30 lines
900 B
Java
30 lines
900 B
Java
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package org.broadinstitute.sting.alignment;
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import org.junit.Test;
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import org.broadinstitute.sting.WalkerTest;
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import java.util.Arrays;
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import java.util.List;
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import java.io.File;
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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 = "ed098018ffcbd055bee966466044428a";
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-R /humgen/gsa-scr1/GATK_Data/bwa/human_b36_both.fasta" +
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" -T Align" +
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" -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878_Pilot1_20.trimmed.unmapped.bam" +
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" -ob %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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