40 lines
1.3 KiB
Java
40 lines
1.3 KiB
Java
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package org.broadinstitute.sting.oneoffprojects.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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* IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
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*
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* @Author chartl
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* @Date Feb 25, 2010
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*/
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public class CoverageStatisticsIntegrationTest extends WalkerTest {
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private boolean RUN_TESTS = false;
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private String root = "-T CoverageStatistics ";
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private String buildRootCmd(String ref, String bam, String interval) {
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return root + "-R "+ref+" -I "+bam+" -L "+interval+" -o %s";
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}
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private void execute(String name, WalkerTestSpec spec) {
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if ( RUN_TESTS ) {
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executeTest(name,spec);
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}
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}
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@Test
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public void testBaseOutputNoFiltering() {
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String bam_file = "/humgen/gsa-hphome1/chartl/projects/depthOfCoverage/testFiles/bams/Ciliopathies_1_88534_3_samples.bam";
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String interval_list = "chr1:855534";
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String reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
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String cmd = buildRootCmd(reference,bam_file,interval_list) + " -mmq 0 -mbq 0 -omitSampleSummary -omitIntervals -omitLocus";
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String expected = "2aee1dbcb69bf1e874d56cd23336afa8";
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WalkerTestSpec spec = new WalkerTestSpec(cmd,1, Arrays.asList(expected));
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execute("testBaseOutputNoFiltering",spec);
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}
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}
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