diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java new file mode 100755 index 000000000..660dfd079 --- /dev/null +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java @@ -0,0 +1,25 @@ +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 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", ""); } +} \ No newline at end of file