38 lines
1.4 KiB
Java
38 lines
1.4 KiB
Java
package org.broadinstitute.sting.gatk.walkers;
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import org.broadinstitute.sting.WalkerTest;
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import org.testng.annotations.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 " + validationDataLocation + "FHS_Pileup_Test.bam "
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+ "-R " + hg18Reference
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+ " -L chr15:46,347,148 -o %s";
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String expected_md5 = "872e89df166b90e06dd2737535c5d8b3";
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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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@Test
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public void testExtendedEventPileup() {
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String gatk_args = "-T Pileup -I " + validationDataLocation + "OV-0930.normal.chunk.bam "
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+ "-R " + hg18Reference
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+ " -show_indels -o %s";
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String expected_md5="06eedc2e7927650961d99d703f4301a4";
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WalkerTestSpec spec = new WalkerTestSpec(gatk_args,1,Arrays.asList(expected_md5));
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executeTest("Testing the extended pileup with indel records included on a small chunk of Ovarian dataset with 20 indels (1 D, 19 I)", spec);
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}
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}
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