27 lines
961 B
Java
27 lines
961 B
Java
package org.broadinstitute.sting.gatk.walkers;
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import org.broadinstitute.sting.WalkerTest;
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import org.junit.Test;
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import java.util.Arrays;
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/**
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* Created by IntelliJ IDEA.
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* User: chartl
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* Date: Dec 1, 2009
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* Time: 9:03:34 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class PileupWalkerIntegrationTest extends WalkerTest {
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@Test
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public void testGnarleyFHSPileup() {
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String gatk_args = "-T Pileup -I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_Pileup_Test.bam "
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+ "-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"
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+ " -L chr15:46,347,148 -o %s";
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String expected_md5 = "59edd722be96402be9dacd4c6f0b0c5e";
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WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5));
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executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases", spec);
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}
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}
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