@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);
}
@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(dataProvider = "assemblyResults")
public void testAddManyHaplotypes(
final java.util.List<AssemblyResult> assemblyResults,
final java.util.List<java.util.List<Haplotype>> haplotypes) {
final AssemblyResultSet subject = new AssemblyResultSet();
for (int i = 0; i < haplotypes.size(); i++) {
final int haplotypeCountBefore = subject.getHaplotypeCount();
final java.util.List<Haplotype> haplos = haplotypes.get(i);
final AssemblyResult ar = assemblyResults.get(i);
for (final Haplotype h : haplos) {
Assert.assertTrue(subject.add(h, ar));
Assert.assertFalse(subject.add(h, ar));
if (h.isReference()) Assert.assertEquals(subject.getReferenceHaplotype(), h);
}
final int haplotypeCountAfter = subject.getHaplotypeCount();
Assert.assertEquals(haplos.size(), haplotypeCountAfter - haplotypeCountBefore);
Assert.assertTrue(subject.getMaximumKmerSize() >= ar.getKmerSize());
Assert.assertTrue(subject.getMinimumKmerSize() <= ar.getKmerSize());
Assert.assertEquals(
subject.getUniqueReadThreadingGraph(ar.getKmerSize()), ar.getThreadingGraph());
}
}