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Merge pull request #516 from broadinstitute/dr_reenable_tests_failing_due_to_java_update 

Re-enable tests that were failing post-maven due to changes in Java's Math.pow() implementation
This commit is contained in:
Eric Banks 2014-02-13 21:05:18 -05:00
parent 238bf4e71d 4b4b93ad1b
commit 7095a60c8e
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",
"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 +

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
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