@Test
public void testGetAltAlleles() throws Exception {

    PerAlleleCollection<Integer> alleleCounts = PerAlleleCollection.createPerAltAlleleCollection();
    Allele altA = Allele.create("A", false);
    Allele altC = Allele.create("C", false);
    Allele altG = Allele.create("G", false);
    Allele altT = Allele.create("T", false);
    Allele[] altAlleles = {altA, altC, altG, altT};
    for (Allele altAllele : altAlleles ) {
        alleleCounts.set(altAllele, 3);
    }
    for (Allele altAllele : altAlleles ) {
        assertTrue(alleleCounts.getAltAlleles().contains(altAllele));
    }
    assertFalse(alleleCounts.getAltAlleles().contains(Allele.create("A", true)));
}