diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalculationModelUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java similarity index 96% rename from protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalculationModelUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java index b1dc423a2..ea57c93c4 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalculationModelUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java @@ -14,7 +14,7 @@ import org.testng.annotations.Test; import java.util.*; -public class ExactAFCalculationModelUnitTest extends BaseTest { +public class AFCalcUnitTest extends BaseTest { static Allele A = Allele.create("A", true); static Allele C = Allele.create("C"); static Allele G = Allele.create("G"); @@ -27,6 +27,7 @@ public class ExactAFCalculationModelUnitTest extends BaseTest { final private static boolean INCLUDE_BIALLELIC = true; final private static boolean INCLUDE_TRIALLELIC = true; final private static boolean Guillermo_FIXME = false; // TODO -- can only be enabled when GdA fixes bug + final private static boolean DEBUG_ONLY = true; @BeforeSuite public void before() { @@ -157,7 +158,7 @@ public class ExactAFCalculationModelUnitTest extends BaseTest { @DataProvider(name = "badGLs") public Object[][] createBadGLs() { - final List genotypes = Arrays.asList(AB2, CC2, CC2, CC2); + final List genotypes = Arrays.asList(AB2, BB2, CC2, CC2); final int nSamples = genotypes.size(); final AFCalc indCalc = AFCalcFactory.createAFCalc(AFCalcFactory.Calculation.EXACT_INDEPENDENT, nSamples, 4); @@ -172,13 +173,13 @@ public class ExactAFCalculationModelUnitTest extends BaseTest { return GetGLsTest.getTests(GetGLsTest.class); } - @Test(enabled = true, dataProvider = "wellFormedGLs") + @Test(enabled = true && ! DEBUG_ONLY, dataProvider = "wellFormedGLs") public void testBiallelicGLs(GetGLsTest cfg) { if ( cfg.getAlleles().size() == 2 ) testResultSimple(cfg); } - @Test(enabled = true, dataProvider = "wellFormedGLs") + @Test(enabled = true && ! DEBUG_ONLY, dataProvider = "wellFormedGLs") public void testTriallelicGLs(GetGLsTest cfg) { if ( cfg.getAlleles().size() > 2 ) testResultSimple(cfg); @@ -241,7 +242,7 @@ public class ExactAFCalculationModelUnitTest extends BaseTest { return tests.toArray(new Object[][]{}); } - @Test(enabled = true, dataProvider = "GLsWithNonInformative", dependsOnMethods = {"testBiallelicGLs", "testTriallelicGLs"}) + @Test(enabled = true && ! DEBUG_ONLY, dataProvider = "GLsWithNonInformative", dependsOnMethods = {"testBiallelicGLs", "testTriallelicGLs"}) public void testGLsWithNonInformative(GetGLsTest onlyInformative, GetGLsTest withNonInformative) { final AFCalcResult expected = onlyInformative.execute(); final AFCalcResult actual = withNonInformative.execute(); @@ -293,7 +294,7 @@ public class ExactAFCalculationModelUnitTest extends BaseTest { } } - @Test(enabled = true, dataProvider = "Models") + @Test(enabled = true && ! DEBUG_ONLY, dataProvider = "Models") public void testLargeGLs(final ExactAFCalc calc) { final Genotype BB = makePL(Arrays.asList(C, C), 20000000, 20000000, 0); GetGLsTest cfg = new GetGLsTest(calc, 1, Arrays.asList(BB, BB, BB), FLAT_3SAMPLE_PRIORS, "flat"); @@ -304,7 +305,7 @@ public class ExactAFCalculationModelUnitTest extends BaseTest { Assert.assertEquals(calculatedAlleleCount, 6); } - @Test(enabled = true, dataProvider = "Models") + @Test(enabled = true && ! DEBUG_ONLY, dataProvider = "Models") public void testMismatchedGLs(final ExactAFCalc calc) { final Genotype AB = makePL(Arrays.asList(A, C), 2000, 0, 2000, 2000, 2000, 2000); final Genotype AC = makePL(Arrays.asList(A, G), 100, 100, 100, 0, 100, 100); @@ -408,7 +409,7 @@ public class ExactAFCalculationModelUnitTest extends BaseTest { return tests.toArray(new Object[][]{}); } - @Test(enabled = true, dataProvider = "PNonRef") + @Test(enabled = true && ! DEBUG_ONLY, dataProvider = "PNonRef") private void testPNonRef(final VariantContext vcRoot, AFCalcFactory.Calculation modelType, ExactAFCalculationTestBuilder.PriorType priorType, @@ -446,7 +447,7 @@ public class ExactAFCalculationModelUnitTest extends BaseTest { return tests.toArray(new Object[][]{}); } - @Test(enabled = true, dataProvider = "Models") + @Test(enabled = true && ! DEBUG_ONLY, dataProvider = "Models") public void testBiallelicPriors(final AFCalc model) { final int REF_PL = 10; final Genotype AB = makePL(Arrays.asList(A,C), REF_PL, 0, 10000); diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ConstrainedAFCalculationModelUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ConstrainedAFCalculationModelUnitTest.java index 674f6f642..4d0034a0f 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ConstrainedAFCalculationModelUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ConstrainedAFCalculationModelUnitTest.java @@ -20,7 +20,7 @@ public class ConstrainedAFCalculationModelUnitTest extends BaseTest { static Allele G = Allele.create("G"); protected static Genotype makePL(final List expectedGT, int ... pls) { - return ExactAFCalculationModelUnitTest.makePL(expectedGT, pls); + return AFCalcUnitTest.makePL(expectedGT, pls); } @DataProvider(name = "MaxACsToVisit") diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java index 22c429e0b..6a10d8fda 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java @@ -84,7 +84,7 @@ public class IndependentAllelesDiploidExactAFCalcUnitTest extends BaseTest { } private Genotype makePL(final int ... PLs) { - return ExactAFCalculationModelUnitTest.makePL(Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), PLs); + return AFCalcUnitTest.makePL(Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), PLs); } @Test(enabled = true, dataProvider = "TestCombineGLs")