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AFCalcUnit test a more appropriate name

This commit is contained in:
Mark DePristo 2012-10-11 12:56:53 -04:00
parent cb857d1640
commit 2d72265f7d
3 changed files with 12 additions and 11 deletions
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19
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalculationModelUnitTest.java → protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java
View File

@ -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<Genotype> genotypes = Arrays.asList(AB2, CC2, CC2, CC2);
final List<Genotype> 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);

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ConstrainedAFCalculationModelUnitTest.java
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@ -20,7 +20,7 @@ public class ConstrainedAFCalculationModelUnitTest extends BaseTest {
static Allele G = Allele.create("G");
protected static Genotype makePL(final List<Allele> expectedGT, int ... pls) {
return ExactAFCalculationModelUnitTest.makePL(expectedGT, pls);
return AFCalcUnitTest.makePL(expectedGT, pls);
}
@DataProvider(name = "MaxACsToVisit")

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java
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@ -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")