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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).
This commit is contained in:
David Roazen 2014-02-12 14:51:51 -05:00
parent 6facf695ab
commit 4b4b93ad1b
2 changed files with 7 additions and 7 deletions
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10
protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -89,9 +89,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
} }
VRTest lowPass = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf", VRTest lowPass = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
"6f029dc7d16e63e19c006613cd0a5cff", // tranches "41e2d951a17de433fe378bb3d9ec75d4", // tranches
"73c7897441622c9b37376eb4f071c560", // recal file "04336b2453202f286da05b69e57f66ed", // recal file
"11a28df79b92229bd317ac49a3ed0fa1"); // cut VCF "d29fd0bdc1c8c3a171e10d29f7ffeaec"); // cut VCF
VRTest lowPassPlusExomes = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf", VRTest lowPassPlusExomes = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf", validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf",
@ -109,7 +109,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
return new Object[][]{ {lowPassPlusExomes} }; return new Object[][]{ {lowPassPlusExomes} };
} }
@Test(dataProvider = "VRTest", enabled = false) @Test(dataProvider = "VRTest")
public void testVariantRecalibrator(VRTest params) { public void testVariantRecalibrator(VRTest params) {
//System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile); //System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile);
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -129,7 +129,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst(); executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst();
} }
@Test(dataProvider = "VRTest",dependsOnMethods="testVariantRecalibrator", enabled = false) @Test(dataProvider = "VRTest",dependsOnMethods="testVariantRecalibrator")
public void testApplyRecalibration(VRTest params) { public void testApplyRecalibration(VRTest params) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b37KGReference + "-R " + b37KGReference +

4
public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MWUnitTest.java
View File

@ -43,7 +43,7 @@ public class MWUnitTest extends BaseTest {
@BeforeClass @BeforeClass
public void init() { } public void init() { }
@Test(enabled = false) @Test
private void testMWU() { private void testMWU() {
logger.warn("Testing MWU"); logger.warn("Testing MWU");
MannWhitneyU mwu = new MannWhitneyU(); 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 // 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.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,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,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 Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,11L,false,cm).second,0.08547008547008,1e-14); // r does a correction, subtracting 1 from U