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Cleaned up and fleshed out unit tests for the Inbreeding Coefficient annotation class.

This commit is contained in:
Eric Banks 2014-09-08 11:40:39 -04:00
parent 56a2554bb0
commit 5e490362ca
1 changed files with 87 additions and 9 deletions
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96
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java
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@ -62,18 +62,19 @@ import java.util.List;
*/
public class InbreedingCoeffUnitTest {
private static double DELTA_PRECISION = 0.001;
Allele Aref, T, C, G, Cref, ATC, ATCATC;
private Allele Aref, T, C;
private int[] hetPLs, homRefPLs;
@BeforeSuite
public void setup() {
// alleles
Aref = Allele.create("A", true);
Cref = Allele.create("C", true);
T = Allele.create("T");
C = Allele.create("C");
G = Allele.create("G");
ATC = Allele.create("ATC");
ATCATC = Allele.create("ATCATC");
// simulating 20 reads with Q30 base qualities
hetPLs = new int[] {240, 0, 240};
homRefPLs = new int[] {0, 60, 600};
}
private Genotype makeGwithPLs(String sample, Allele a1, Allele a2, double[] pls) {
@ -89,10 +90,6 @@ public class InbreedingCoeffUnitTest {
return gt;
}
private Genotype makeG(String sample, Allele a1, Allele a2) {
return GenotypeBuilder.create(sample, Arrays.asList(a1, a2));
}
private Genotype makeG(String sample, Allele a1, Allele a2, int... pls) {
return new GenotypeBuilder(sample, Arrays.asList(a1, a2)).PL(pls).make();
}
@ -137,4 +134,85 @@ public class InbreedingCoeffUnitTest {
final double ICresult2 = new InbreedingCoeff().calculateIC(test2, test2.getGenotypes());
Assert.assertEquals(ICresult2, -1.0, DELTA_PRECISION, "Pass");
}
@Test
public void testSingletonVsCommonAllele() {
final List<Genotype> allGTs = new ArrayList<>();
final int numHomRefGTs = 10000;
for ( int i = 0; i < numHomRefGTs; i++ )
allGTs.add(makeG("ref" + i, Aref, Aref, homRefPLs));
allGTs.add(makeG("het0", Aref, T, hetPLs));
int numHetGTs = 1;
final VariantContext singleton = makeVC("singleton", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
final double ICsingleton = new InbreedingCoeff().calculateIC(singleton, singleton.getGenotypes());
final int targetNumHetGTs = 20;
for ( int i = numHetGTs; i < targetNumHetGTs; i++ )
allGTs.add(makeG("het" + i, Aref, T, hetPLs));
final VariantContext common = makeVC("common", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
final double ICcommon = new InbreedingCoeff().calculateIC(common, common.getGenotypes());
Assert.assertTrue(Math.abs(ICsingleton) < Math.abs(ICcommon), String.format("singleton=%f common=%f", ICsingleton, ICcommon));
}
@Test
public void testLargeCohorts() {
final List<Genotype> allGTs = new ArrayList<>();
final int numHomRefGTs = 1000000;
for ( int i = 0; i < numHomRefGTs; i++ )
allGTs.add(makeG("ref" + i, Aref, Aref, homRefPLs));
allGTs.add(makeG("het0", Aref, T, hetPLs));
int numHetGTs = 1;
final VariantContext singleton = makeVC("singleton", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
final double ICsingleton = new InbreedingCoeff().calculateIC(singleton, singleton.getGenotypes());
for ( int i = numHetGTs; i < 100; i++ ) {
allGTs.add(makeG("het" + i, Aref, T, hetPLs));
numHetGTs++;
}
final VariantContext hundredton = makeVC("hundredton", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
final double IChundredton = new InbreedingCoeff().calculateIC(hundredton, hundredton.getGenotypes());
Assert.assertTrue(Math.abs(ICsingleton) < Math.abs(IChundredton), String.format("singleton=%f hundredton=%f", ICsingleton, IChundredton));
for ( int i = numHetGTs; i < numHomRefGTs; i++ )
allGTs.add(makeG("het" + i, Aref, T, hetPLs));
final VariantContext common = makeVC("common", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
final double ICcommon = new InbreedingCoeff().calculateIC(common, common.getGenotypes());
Assert.assertTrue(Math.abs(IChundredton) < Math.abs(ICcommon), String.format("hundredton=%f common=%f", IChundredton, ICcommon));
}
@Test
public void testAllHetsForLargeCohorts() {
final int numGTs = 1000000;
final List<Genotype> singletonGTs = new ArrayList<>();
for ( int i = 0; i < numGTs; i++ )
singletonGTs.add(makeG("ref" + i, Aref, Aref, homRefPLs));
singletonGTs.add(makeG("het0", Aref, T, hetPLs));
final VariantContext singleton = makeVC("singleton", Arrays.asList(Aref, T), singletonGTs.toArray(new Genotype[singletonGTs.size()]));
final double ICsingleton = new InbreedingCoeff().calculateIC(singleton, singleton.getGenotypes());
final List<Genotype> allHetGTs = new ArrayList<>();
for ( int i = 0; i < numGTs; i++ )
allHetGTs.add(makeG("het" + i, Aref, T, hetPLs));
final VariantContext allHet = makeVC("allHet", Arrays.asList(Aref, T), allHetGTs.toArray(new Genotype[allHetGTs.size()]));
final double ICHets = new InbreedingCoeff().calculateIC(allHet, allHet.getGenotypes());
Assert.assertTrue(Math.abs(ICsingleton) < Math.abs(ICHets), String.format("singleton=%f allHets=%f", ICsingleton, ICHets));
}
}