/**
* Test that the contents of an allele-list are the ones expected.
*
* <p>
*
* <p>This method perform various consistency check involving all the {@link
* org.broadinstitute.gatk.utils.genotyper.AlleleList} interface methods. Therefore calling this
* method is equivalent to a thorough check of the {@link
* org.broadinstitute.gatk.utils.genotyper.AlleleList} aspect of the {@code actual} argument.
*
* @param actual the sample-list to assess.
* @param expected the expected sample-list.
* @throws IllegalArgumentException if {@code expected} is {@code null} or contains {@code null}s
* which is an indication of an bug in the testing code.
* @throws RuntimeException if there is some testing assertion exception which is an indication of
* an actual bug the code that is been tested.
*/
public static <A extends Allele> void assertAlleleList(
final AlleleList<A> actual, final List<A> expected) {
if (expected == null) throw new IllegalArgumentException("the expected list cannot be null");
final Set<A> expectedAlleleSet = new HashSet<>(expected.size());
Assert.assertNotNull(actual);
Assert.assertEquals(actual.alleleCount(), expected.size());
for (int i = 0; i < expected.size(); i++) {
final A expectedAllele = expected.get(i);
if (expectedAllele == null)
throw new IllegalArgumentException("the expected sample cannot be null");
if (expectedAllele.equals(NEVER_USE_ALLELE))
throw new IllegalArgumentException("you cannot use the forbidden sample name");
if (expectedAlleleSet.contains(expected.get(i)))
throw new IllegalArgumentException(
"repeated allele in the expected list, this is a test bug");
final A actualAllele = actual.alleleAt(i);
Assert.assertNotNull(actualAllele, "allele cannot be null");
Assert.assertFalse(
expectedAlleleSet.contains(actualAllele), "repeated allele: " + actualAllele);
Assert.assertEquals(actualAllele, expectedAllele, "wrong allele order; index = " + i);
Assert.assertEquals(actual.alleleIndex(actualAllele), i, "allele index mismatch");
expectedAlleleSet.add(actualAllele);
}
Assert.assertEquals(actual.alleleIndex((A) NEVER_USE_ALLELE), -1);
}
/**
* Generate testing alleles.
*
* <p>Basically all are random alleles given the maximum allele length.
*
* <p>So with a low max-allele-length and high allele-count you can force repeats.
*
* @param alleleCount number of alleles to generate.
* @param maxAlleleLength the maximum length of the allele in bases.
* @param skipIfRepeats throw an test-skip exception {@link SkipException} if the resulting
* allele-list has repeats, thus is size is less than {@code alleleCount}
* @throws RuntimeException if {@code alleleCount} is negative or {@code maxAlleleLength} is less
* than 1.
* @return never {@code null}.
*/
static AlleleList<Allele> alleleList(
final int alleleCount, final int maxAlleleLength, final boolean skipIfRepeats) {
final Allele[] alleles =
AlleleListUnitTester.generateRandomAlleles(alleleCount, maxAlleleLength);
if (alleleCount > 0) alleles[0] = Allele.create(alleles[0].getBases(), true);
final AlleleList<Allele> alleleList = new IndexedAlleleList<>(alleles);
if (skipIfRepeats && alleleList.alleleCount() != alleles.length)
throw new SkipException("repeated alleles, should be infrequent");
return alleleList;
}
