diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index c30ef43e5..c4de50b25 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -89,9 +89,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { } VRTest lowPass = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf", - "6f029dc7d16e63e19c006613cd0a5cff", // tranches - "73c7897441622c9b37376eb4f071c560", // recal file - "11a28df79b92229bd317ac49a3ed0fa1"); // cut VCF + "41e2d951a17de433fe378bb3d9ec75d4", // tranches + "04336b2453202f286da05b69e57f66ed", // recal file + "d29fd0bdc1c8c3a171e10d29f7ffeaec"); // cut VCF VRTest lowPassPlusExomes = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf", validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf", @@ -109,7 +109,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { return new Object[][]{ {lowPassPlusExomes} }; } - @Test(dataProvider = "VRTest", enabled = false) + @Test(dataProvider = "VRTest") public void testVariantRecalibrator(VRTest params) { //System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -129,7 +129,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst(); } - @Test(dataProvider = "VRTest",dependsOnMethods="testVariantRecalibrator", enabled = false) + @Test(dataProvider = "VRTest",dependsOnMethods="testVariantRecalibrator") public void testApplyRecalibration(VRTest params) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b37KGReference + diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MWUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MWUnitTest.java index d29f448d6..312e4d5b1 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MWUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MWUnitTest.java @@ -43,7 +43,7 @@ public class MWUnitTest extends BaseTest { @BeforeClass public void init() { } - @Test(enabled = false) + @Test private void testMWU() { logger.warn("Testing MWU"); MannWhitneyU mwu = new MannWhitneyU(); @@ -93,7 +93,7 @@ public class MWUnitTest extends BaseTest { // tests using the hypothesis that set 1 dominates set 2 (U value = 30) -- empirical should be identical, normall approx close, uniform way off Assert.assertEquals(MannWhitneyU.calculatePNormalApproximation(sizes.second,sizes.first,30L,true).second,2.0*0.08216463976903321,1e-14); - Assert.assertEquals(MannWhitneyU.calculatePUniformApproximation(sizes.second,sizes.first,30L),0.0023473625009328147,1e-14); + Assert.assertEquals(MannWhitneyU.calculatePUniformApproximation(sizes.second,sizes.first,30L),0.0023473625009559074,1e-14); Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,30L,false,pm).second,0.021756021756021756,1e-14); // note -- exactly same value as above Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,29L,false,cm).second,1.0-0.08547008547008,1e-14); // r does a correction, subtracting 1 from U Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,11L,false,cm).second,0.08547008547008,1e-14); // r does a correction, subtracting 1 from U