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Integration tests for count duplicates walker validated on a TCGA hybrid capture lane. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2459 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-12-28 23:57:25 +00:00
parent fcc80e8632
commit 9d263b2565
1 changed files with 25 additions and 0 deletions
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java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java 100755
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package org.broadinstitute.sting.playground.gatk.walkers.duplicates;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.io.File;
import java.util.Arrays;
import java.util.List;
public class DuplicatesWalkersIntegrationTest extends WalkerTest {
public void testClipper(String name, String args, String md5) {
WalkerTestSpec spec = new WalkerTestSpec(
"-T CountDuplicates " +
"-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " +
"-I /humgen/gsa-hpprojects/GATK/data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam " +
"-o %s " + args,
1, // just one output file
Arrays.asList("tmp"),
Arrays.asList(md5));
List<File> result = executeTest(name, spec).getFirst();
}
@Test public void testChr110Mb() { testClipper("testChr1-10mb", "-L chr1:1-10,000,000 --quiet", ""); }
@Test public void testIntervalVerbose() { testClipper("testIntervalVerbose", "-L chr1:6,527,154-6,528,292", ""); }
}