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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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

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