49 lines
2.3 KiB
Java
49 lines
2.3 KiB
Java
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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.HashMap;
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import java.util.Map;
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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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public class DepthOfCoverageIntegrationTest extends WalkerTest {
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private static String root = "-L 1:10,164,500-10,164,520 -R /broad/1KG/reference/human_b36_both.fasta -T DepthOfCoverage -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam";
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static HashMap<String, String> expectations = new HashMap<String, String>();
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static {
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expectations.put("-s COMPACT -minMAPQ 1", "a6b2005e37f48545e9604e0f809cf618");
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expectations.put("-s COMPACT", "c3cd44717487ad3c7d6d969583d9bb8c");
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expectations.put("-s COMPACT -ed", "73aacc9febea393a4c3760bd6c70a557");
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expectations.put("-s NONE", "628201adcef01e8bc3e9cdf96b86003b");
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expectations.put("-s NONE -minMAPQ 1", "2425ccbcfdfb9e9a98fcf30c6f2bfcdd");
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expectations.put("-s NONE -minMAPQ 100", "09eaf5a4c811e4ac74de5d179a9ffbe7");
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expectations.put("-s DETAILED -minMAPQ 1", "9059436a57f8c28ef16ee9b2c7cd3ebb");
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expectations.put("-s DETAILED", "fac3bb643f34eb9d90dac0e0358b55ab");
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expectations.put("-s DETAILED -ed", "4d991221aa5e206de11878e88c380de1");
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}
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@Test
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public void testDepthOfCoverage1() {
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for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
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String extraArgs = entry.getKey();
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String md5 = entry.getValue();
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WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s",
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1, // just one output file
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Arrays.asList(md5));
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executeTest("testDepthOfCoverage1", spec);
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}
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}
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@Test
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public void testDepthOfCoverage454() {
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WalkerTestSpec spec = new WalkerTestSpec(
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"-T DepthOfCoverage -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam -L 1:10,001,890-10,001,895 -s DETAILED -o %s",
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1, // just one output file
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Arrays.asList("5c94916ec193ca825c681dd0175c6164"));
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executeTest("testDepthOfCoverage454", spec);
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}
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}
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