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Added Unit tests for new methods in GenotypeLikelihoods

This commit is contained in:
Laurent Francioli 2011-11-14 10:47:02 +01:00
parent 571c724cfd
commit 34acf8b978
1 changed files with 47 additions and 0 deletions
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47
public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java
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@ -29,10 +29,13 @@ package org.broadinstitute.sting.utils.variantcontext;
// the imports for unit testing.
import org.broadinstitute.sting.utils.MathUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import java.util.EnumMap;
/**
* Basic unit test for Genotype likelihoods objects
@ -69,6 +72,50 @@ public class GenotypeLikelihoodsUnitTest {
gl.getAsVector();
}
@Test
public void testGetAsMap(){
GenotypeLikelihoods gl = new GenotypeLikelihoods(v);
//Log scale
EnumMap<Genotype.Type,Double> glMap = gl.getAsMap(false);
Assert.assertEquals(v[Genotype.Type.HOM_REF.ordinal()-1],glMap.get(Genotype.Type.HOM_REF));
Assert.assertEquals(v[Genotype.Type.HET.ordinal()-1],glMap.get(Genotype.Type.HET));
Assert.assertEquals(v[Genotype.Type.HOM_VAR.ordinal()-1],glMap.get(Genotype.Type.HOM_VAR));
//Linear scale
glMap = gl.getAsMap(true);
double [] vl = MathUtils.normalizeFromLog10(v);
Assert.assertEquals(vl[Genotype.Type.HOM_REF.ordinal()-1],glMap.get(Genotype.Type.HOM_REF));
Assert.assertEquals(vl[Genotype.Type.HET.ordinal()-1],glMap.get(Genotype.Type.HET));
Assert.assertEquals(vl[Genotype.Type.HOM_VAR.ordinal()-1],glMap.get(Genotype.Type.HOM_VAR));
//Test missing likelihoods
gl = new GenotypeLikelihoods(".");
glMap = gl.getAsMap(false);
Assert.assertNull(glMap);
}
@Test
public void testGetNegLog10GQ(){
GenotypeLikelihoods gl = new GenotypeLikelihoods(vPLString);
//GQ for the best guess genotype
Assert.assertEquals(gl.getNegLog10GQ(Genotype.Type.HET),3.9);
double[] test = MathUtils.normalizeFromLog10(gl.getAsVector());
//GQ for the other genotypes
Assert.assertEquals(gl.getNegLog10GQ(Genotype.Type.HOM_REF), -1.0 * Math.log10(1.0 - test[Genotype.Type.HOM_REF.ordinal()-1]));
Assert.assertEquals(gl.getNegLog10GQ(Genotype.Type.HOM_VAR), -1.0 * Math.log10(1.0 - test[Genotype.Type.HOM_VAR.ordinal()-1]));
//Test missing likelihoods
gl = new GenotypeLikelihoods(".");
Assert.assertEquals(gl.getNegLog10GQ(Genotype.Type.HOM_REF),Double.NEGATIVE_INFINITY);
Assert.assertEquals(gl.getNegLog10GQ(Genotype.Type.HET),Double.NEGATIVE_INFINITY);
Assert.assertEquals(gl.getNegLog10GQ(Genotype.Type.HOM_VAR),Double.NEGATIVE_INFINITY);
}
private void assertDoubleArraysAreEqual(double[] v1, double[] v2) {
Assert.assertEquals(v1.length, v2.length);
for ( int i = 0; i < v1.length; i++ ) {