// 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 GenotypesContext stripPLs(GenotypesContext genotypes) {
GenotypesContext newGs = GenotypesContext.create(genotypes.size());
for (final Genotype g : genotypes) {
newGs.add(g.hasLikelihoods() ? removePLs(g) : g);
}
return newGs;
}
/** @return the number of samples in the context */
public int getNSamples() {
return genotypes.size();
}