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Add tests for non-informative samples in ExactAFCalculationModel

This commit is contained in:
Mark DePristo 2012-10-01 13:03:08 -05:00
parent de941ddbbe
commit 33c7841c4d
1 changed files with 75 additions and 7 deletions
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82
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModelUnitTest.java
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@ -8,10 +8,7 @@ import org.testng.annotations.BeforeSuite;
import org.testng.annotations.DataProvider; import org.testng.annotations.DataProvider;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.util.ArrayList; import java.util.*;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
public class ExactAFCalculationModelUnitTest extends BaseTest { public class ExactAFCalculationModelUnitTest extends BaseTest {
@ -21,8 +18,8 @@ public class ExactAFCalculationModelUnitTest extends BaseTest {
static Allele T = Allele.create("T"); static Allele T = Allele.create("T");
static int sampleNameCounter = 0; static int sampleNameCounter = 0;
static Genotype AA1, AB1, BB1; static Genotype AA1, AB1, BB1, NON_INFORMATIVE1;
static Genotype AA2, AB2, AC2, BB2, BC2, CC2; static Genotype AA2, AB2, AC2, BB2, BC2, CC2, NON_INFORMATIVE2;
final double[] FLAT_3SAMPLE_PRIORS = new double[2*3+1]; // flat priors final double[] FLAT_3SAMPLE_PRIORS = new double[2*3+1]; // flat priors
@BeforeSuite @BeforeSuite
@ -30,6 +27,7 @@ public class ExactAFCalculationModelUnitTest extends BaseTest {
AA1 = makePL(Arrays.asList(A, A), 0, 20, 20); AA1 = makePL(Arrays.asList(A, A), 0, 20, 20);
AB1 = makePL(Arrays.asList(A, C), 20, 0, 20); AB1 = makePL(Arrays.asList(A, C), 20, 0, 20);
BB1 = makePL(Arrays.asList(C, C), 20, 20, 0); BB1 = makePL(Arrays.asList(C, C), 20, 20, 0);
NON_INFORMATIVE1 = makePL(Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 0, 0, 0);
AA2 = makePL(Arrays.asList(A, A), 0, 20, 20, 20, 20, 20); AA2 = makePL(Arrays.asList(A, A), 0, 20, 20, 20, 20, 20);
AB2 = makePL(Arrays.asList(A, C), 20, 0, 20, 20, 20, 20); AB2 = makePL(Arrays.asList(A, C), 20, 0, 20, 20, 20, 20);
@ -37,6 +35,7 @@ public class ExactAFCalculationModelUnitTest extends BaseTest {
AC2 = makePL(Arrays.asList(A, G), 20, 20, 20, 0, 20, 20); AC2 = makePL(Arrays.asList(A, G), 20, 20, 20, 0, 20, 20);
BC2 = makePL(Arrays.asList(C, G), 20, 20, 20, 20, 0, 20); BC2 = makePL(Arrays.asList(C, G), 20, 20, 20, 20, 0, 20);
CC2 = makePL(Arrays.asList(G, G), 20, 20, 20, 20, 20, 0); CC2 = makePL(Arrays.asList(G, G), 20, 20, 20, 20, 20, 0);
NON_INFORMATIVE2 = makePL(Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 0, 0, 0, 0, 0, 0);
} }
private Genotype makePL(final List<Allele> expectedGT, int ... pls) { private Genotype makePL(final List<Allele> expectedGT, int ... pls) {
@ -104,7 +103,8 @@ public class ExactAFCalculationModelUnitTest extends BaseTest {
} }
public String toString() { public String toString() {
return String.format("%s model=%s input=%s", super.toString(), calc.getClass().getSimpleName(), GLs); return String.format("%s model=%s input=%s", super.toString(), calc.getClass().getSimpleName(),
GLs.size() > 5 ? String.format("%d samples", GLs.size()) : GLs);
} }
} }
@ -133,9 +133,77 @@ public class ExactAFCalculationModelUnitTest extends BaseTest {
return GetGLsTest.getTests(GetGLsTest.class); return GetGLsTest.getTests(GetGLsTest.class);
} }
private static class NonInformativeData {
final Genotype nonInformative;
final List<Genotype> called;
final int nAltAlleles;
private NonInformativeData(List<Genotype> called, Genotype nonInformative, int nAltAlleles) {
this.called = called;
this.nonInformative = nonInformative;
this.nAltAlleles = nAltAlleles;
}
}
@DataProvider(name = "GLsWithNonInformative")
public Object[][] makeGLsWithNonInformative() {
List<Object[]> tests = new ArrayList<Object[]>();
final List<NonInformativeData> nonInformativeTests = new LinkedList<NonInformativeData>();
nonInformativeTests.add(new NonInformativeData(Arrays.asList(AB1), NON_INFORMATIVE1, 1));
nonInformativeTests.add(new NonInformativeData(Arrays.asList(AB2), NON_INFORMATIVE2, 2));
nonInformativeTests.add(new NonInformativeData(Arrays.asList(AB2, BC2), NON_INFORMATIVE2, 2));
for ( final int nNonInformative : Arrays.asList(1, 10, 100) ) {
for ( final NonInformativeData testData : nonInformativeTests ) {
final List<Genotype> samples = new ArrayList<Genotype>();
samples.addAll(testData.called);
samples.addAll(Collections.nCopies(nNonInformative, testData.nonInformative));
final int nSamples = samples.size();
final DiploidExactAFCalculation diploidCalc = new DiploidExactAFCalculation(nSamples, 4);
final GeneralPloidyExactAFCalculation generalCalc = new GeneralPloidyExactAFCalculation(nSamples, 4, 2);
final double[] priors = new double[2*nSamples+1]; // flat priors
for ( ExactAFCalculation model : Arrays.asList(diploidCalc, generalCalc) ) {
final GetGLsTest onlyInformative = new GetGLsTest(model, testData.nAltAlleles, testData.called, priors);
for ( int rotation = 0; rotation < nSamples; rotation++ ) {
Collections.rotate(samples, 1);
final GetGLsTest withNonInformative = new GetGLsTest(model, testData.nAltAlleles, samples, priors);
tests.add(new Object[]{onlyInformative, withNonInformative});
}
}
}
}
return tests.toArray(new Object[][]{});
}
@Test(dataProvider = "wellFormedGLs") @Test(dataProvider = "wellFormedGLs")
public void testGLs(GetGLsTest cfg) { public void testGLs(GetGLsTest cfg) {
testResultSimple(cfg);
}
@Test(dataProvider = "GLsWithNonInformative", dependsOnMethods = "testGLs")
public void testGLsWithNonInformative(GetGLsTest onlyInformative, GetGLsTest withNonInformative) {
final AlleleFrequencyCalculationResult expected = onlyInformative.execute();
final AlleleFrequencyCalculationResult actual = withNonInformative.execute();
testResultSimple(withNonInformative);
Assert.assertEquals(actual.getLog10PosteriorOfAFzero(), expected.getLog10LikelihoodOfAFzero());
Assert.assertEquals(actual.getLog10LikelihoodOfAFzero(), expected.getLog10LikelihoodOfAFzero());
Assert.assertEquals(actual.getLog10PosteriorsMatrixSumWithoutAFzero(), expected.getLog10PosteriorsMatrixSumWithoutAFzero());
Assert.assertEquals(actual.getAlleleCountsOfMAP(), expected.getAlleleCountsOfMAP());
Assert.assertEquals(actual.getAlleleCountsOfMLE(), expected.getAlleleCountsOfMLE());
Assert.assertEquals(actual.getLog10MAP(), expected.getLog10MAP());
Assert.assertEquals(actual.getLog10MLE(), expected.getLog10MLE());
Assert.assertEquals(actual.getAllelesUsedInGenotyping(), expected.getAllelesUsedInGenotyping());
}
private void testResultSimple(final GetGLsTest cfg) {
final AlleleFrequencyCalculationResult result = cfg.execute(); final AlleleFrequencyCalculationResult result = cfg.execute();
if ( cfg.isNonRef() ) { if ( cfg.isNonRef() ) {