diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java new file mode 100755 index 000000000..446483e07 --- /dev/null +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java @@ -0,0 +1,35 @@ +package org.broadinstitute.sting.gatk.walkers.genotyper; + +import org.broadinstitute.sting.WalkerTest; +import org.junit.Test; + +import java.util.ArrayList; + +public class UnifiedGenotyperPerformanceTest extends WalkerTest { + + @Test + public void testUnifiedGenotyperWholeGenome() { + WalkerTestSpec spec = new WalkerTestSpec( + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + " -T UnifiedGenotyper" + + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + + " -L chr1:1-50,000,000" + + " -varout /dev/null", + 0, + new ArrayList(0)); + executeTest("testUnifiedGenotyperWholeGenome", spec); + } + + @Test + public void testUnifiedGenotyperWholeExome() { + WalkerTestSpec spec = new WalkerTestSpec( + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + " -T UnifiedGenotyper" + + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + + " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + + " -varout /dev/null", + 0, + new ArrayList(0)); + executeTest("testUnifiedGenotyperWholeExome", spec); + } +} \ No newline at end of file