diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLiteIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLiteIntegrationTest.java new file mode 100755 index 000000000..f9a921a86 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLiteIntegrationTest.java @@ -0,0 +1,35 @@ +package org.broadinstitute.sting.gatk.walkers.genotyper; + +import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.testng.annotations.Test; + +import java.io.File; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; + +// ********************************************************************************** // +// Note that this class also serves as an integration test for the VariantAnnotator! // +// ********************************************************************************** // + +public class UnifiedGenotyperLiteIntegrationTest extends WalkerTest { + + private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129; + + // -------------------------------------------------------------------------------------------------------------- + // + // testing contamination down-sampling gets ignored + // + // -------------------------------------------------------------------------------------------------------------- + + @Test + public void testContaminationDownsampling() { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, + Arrays.asList("9addd225a985178339a0c49dc5fdc220")); + executeTest("test contamination_percentage_to_filter gets ignored", spec); + } + +}