45 lines
1.9 KiB
Java
Executable File
45 lines
1.9 KiB
Java
Executable File
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("-minMAPQ 1", "59c6071105a598e19f460640c35768c6");
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expectations.put("-minMAPQ 100", "e997fb5d61eaec21518722b0de90af20");
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expectations.put("-bySample", "160ffa185dbfa8b0d2dc57f60f5b1e48");
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expectations.put("-byRG", "dd3b4d040df7325dad4760ac6fa5252d");
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expectations.put("-minMAPQ 1 -bySample -byRG", "bd2a07ef548b86e82ac6cce534225612");
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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 -o %s",
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1, // just one output file
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Arrays.asList("51203ba5ab928449cd01363af0b91510"));
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executeTest("testDepthOfCoverage454", spec);
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}
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} |