// necessary to not overload equals for genotypes
private void assertGenotypesAreMostlyEqual(GenotypesContext actual, GenotypesContext expected) {
if (actual == expected) {
return;
}
if (actual == null || expected == null) {
Assert.fail("Maps not equal: expected: " + expected + " and actual: " + actual);
}
if (actual.size() != expected.size()) {
Assert.fail("Maps do not have the same size:" + actual.size() + " != " + expected.size());
}
for (Genotype value : actual) {
Genotype expectedValue = expected.get(value.getSampleName());
Assert.assertEquals(
value.getAlleles(), expectedValue.getAlleles(), "Alleles in Genotype aren't equal");
Assert.assertEquals(value.getGQ(), expectedValue.getGQ(), "GQ values aren't equal");
Assert.assertEquals(
value.hasLikelihoods(),
expectedValue.hasLikelihoods(),
"Either both have likelihoods or both not");
if (value.hasLikelihoods())
Assert.assertEquals(
value.getLikelihoods().getAsVector(),
expectedValue.getLikelihoods().getAsVector(),
"Genotype likelihoods aren't equal");
}
}
public static void assertEquals(final Genotype actual, final Genotype expected) {
Assert.assertEquals(actual.getSampleName(), expected.getSampleName(), "Genotype names");
Assert.assertEquals(actual.getAlleles(), expected.getAlleles(), "Genotype alleles");
Assert.assertEquals(
actual.getGenotypeString(), expected.getGenotypeString(), "Genotype string");
Assert.assertEquals(actual.getType(), expected.getType(), "Genotype type");
// filters are the same
Assert.assertEquals(actual.getFilters(), expected.getFilters(), "Genotype fields");
Assert.assertEquals(actual.isFiltered(), expected.isFiltered(), "Genotype isFiltered");
// inline attributes
Assert.assertEquals(actual.getDP(), expected.getDP(), "Genotype dp");
Assert.assertTrue(Arrays.equals(actual.getAD(), expected.getAD()));
Assert.assertEquals(actual.getGQ(), expected.getGQ(), "Genotype gq");
Assert.assertEquals(actual.hasPL(), expected.hasPL(), "Genotype hasPL");
Assert.assertEquals(actual.hasAD(), expected.hasAD(), "Genotype hasAD");
Assert.assertEquals(actual.hasGQ(), expected.hasGQ(), "Genotype hasGQ");
Assert.assertEquals(actual.hasDP(), expected.hasDP(), "Genotype hasDP");
Assert.assertEquals(
actual.hasLikelihoods(), expected.hasLikelihoods(), "Genotype haslikelihoods");
Assert.assertEquals(
actual.getLikelihoodsString(),
expected.getLikelihoodsString(),
"Genotype getlikelihoodsString");
Assert.assertEquals(
actual.getLikelihoods(), expected.getLikelihoods(), "Genotype getLikelihoods");
Assert.assertTrue(Arrays.equals(actual.getPL(), expected.getPL()));
Assert.assertEquals(
actual.getPhredScaledQual(), expected.getPhredScaledQual(), "Genotype phredScaledQual");
assertAttributesEquals(actual.getExtendedAttributes(), expected.getExtendedAttributes());
Assert.assertEquals(actual.isPhased(), expected.isPhased(), "Genotype isPhased");
Assert.assertEquals(actual.getPloidy(), expected.getPloidy(), "Genotype getPloidy");
}
