From 4b4b93ad1be3d52ba64ee9a5a10aa93e23ebafdb Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Wed, 12 Feb 2014 14:51:51 -0500
Subject: [PATCH] Re-enable tests that were failing post-maven due to changes
 in Java's Math.pow() implementation

After extensive detective work, Joel determined that these tests were failing
due to changes in the implementation of Math.pow() in newer versions of
Java 1.7.

All GSA members should ensure that they're using a JDK that is at least
as current as the one in the Java-1.7 dotkit on the Broad servers
(build 1.7.0_51-b13).
---
 .../VariantRecalibrationWalkersIntegrationTest.java    | 10 +++++-----
 .../org/broadinstitute/sting/utils/MWUnitTest.java     |  4 ++--
 2 files changed, 7 insertions(+), 7 deletions(-)

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