31 lines
1.2 KiB
Java
31 lines
1.2 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.testng.annotations.Test;
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import java.util.Arrays;
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public class BAQIntegrationTest extends WalkerTest {
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private final static String baseCommand = "-T PrintReads -R " + b36KGReference +
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" -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" +
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" -o %s" +
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" -L 1:10,000,000-10,100,000";
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// --------------------------------------------------------------------------------------------------------------
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//
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// testing BAQ with SLX, 454, and SOLID data
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//
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// --------------------------------------------------------------------------------------------------------------
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@Test
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public void testPrintReadsNoBAQ() {
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WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("902197bf77ed5a828d50e08771685928"));
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executeTest(String.format("testPrintReadsNoBAQ"), spec);
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}
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@Test
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public void testPrintReadsRecalBAQ() {
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WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("4ac691bde1ba1301a59857694fda6ae2"));
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executeTest(String.format("testPrintReadsRecalBAQ"), spec);
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}
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}
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