@Test
public void testSet() throws Exception {

    PerAlleleCollection<Integer> alleleCounts = PerAlleleCollection.createPerRefAndAltAlleleCollection();
    Allele refA = Allele.create("A", true);
    Allele altT = Allele.create("T", false);
    alleleCounts.set(refA, 40);
    alleleCounts.set(altT, 10);
    assertEquals((int)alleleCounts.getRef(), 40);
    assertEquals((int)alleleCounts.getAlt(altT), 10);
}