@Test(dataProvider = "trimmingData")
public void testTrimTo(
final Map<Haplotype, AssemblyResult> haplotypesAndResultSets, final AssemblyRegion original) {
final AssemblyResultSet subject = new AssemblyResultSet();
for (final Map.Entry<Haplotype, AssemblyResult> entry : haplotypesAndResultSets.entrySet())
subject.add(entry.getKey(), entry.getValue());
subject.setRegionForGenotyping(original);
final GenomeLoc originalLocation = original.getExtendedSpan();
final int length = originalLocation.size();
final GenomeLoc newLocation =
originalLocation.setStop(
originalLocation.setStart(originalLocation, originalLocation.getStart() + length / 2),
originalLocation.getStop() - length / 2);
final AssemblyRegion newRegion = original.trim(newLocation);
final Map<Haplotype, Haplotype> originalHaplotypesByTrimmed =
new HashMap<>(haplotypesAndResultSets.size());
for (final Haplotype h : haplotypesAndResultSets.keySet())
originalHaplotypesByTrimmed.put(h.trim(newRegion.getExtendedSpan()), h);
final AssemblyResultSet trimmed = subject.trimTo(newRegion);
Assert.assertFalse(subject.wasTrimmed());
Assert.assertTrue(trimmed.wasTrimmed());
for (final Haplotype h : trimmed.getHaplotypeList()) {
Assert.assertEquals(h.getGenomeLocation(), newLocation);
Assert.assertEquals(h.getBases().length, newLocation.size());
}
}
@Test
public void testEmptyResultSet() {
final AssemblyResultSet subject = new AssemblyResultSet();
Assert.assertEquals(subject.getHaplotypeList().size(), 0);
Assert.assertEquals(subject.getHaplotypeCount(), 0);
Assert.assertEquals(subject.getReferenceHaplotype(), null);
Assert.assertEquals(subject.getFullReferenceWithPadding(), null);
Assert.assertEquals(subject.getPaddedReferenceLoc(), null);
Assert.assertEquals(subject.getRegionForGenotyping(), null);
Assert.assertEquals(subject.getUniqueReadThreadingGraph(10), null);
Assert.assertFalse(subject.hasMultipleKmerSizes());
}
@Test
public void testAddReferenceHaplotype() {
final Haplotype ref = new Haplotype("ACGT".getBytes(), true);
ref.setGenomeLocation(genomeLocParser.createGenomeLoc("1", 1, ref.length() + 1));
final AssemblyResultSet subject = new AssemblyResultSet();
Assert.assertTrue(subject.add(ref));
Assert.assertFalse(subject.add(ref));
Assert.assertEquals(subject.getReferenceHaplotype(), ref);
Assert.assertEquals(subject.getHaplotypeCount(), 1);
Assert.assertEquals(subject.getHaplotypeList().size(), 1);
}