@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());
}
}
@DataProvider(name = "trimmingData")
public Iterator<Object[]> trimmingData() {
final AssemblyRegion activeRegion =
new AssemblyRegion(
genomeLocParser.createGenomeLoc("1", 1000, 1100), genomeLocParser, 25, header);
final int length = activeRegion.getExtendedSpan().size();
final RandomDNA rnd = new RandomDNA(13); // keep it prepoducible by fixing the seed to lucky 13.
final AssemblyRegionTestDataSet actd =
new AssemblyRegionTestDataSet(
10,
new String(rnd.nextBases(length)),
new String[] {"Civar:*1T*"},
new String[0],
new byte[0],
new byte[0],
new byte[0]);
final List<Haplotype> haplotypes = actd.haplotypeList();
for (final Haplotype h : haplotypes) h.setGenomeLocation(activeRegion.getExtendedSpan());
final ReadThreadingGraph rtg = new ReadThreadingGraph(10);
for (final Haplotype h : haplotypes)
rtg.addSequence("seq-" + Math.abs(h.hashCode()), h.getBases(), h.isReference());
final SeqGraph seqGraph = rtg.toSequenceGraph();
final AssemblyResult ar =
new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, seqGraph, rtg);
final Map<Haplotype, AssemblyResult> result = new HashMap<>();
for (final Haplotype h : haplotypes) result.put(h, ar);
return Collections.singleton(new Object[] {result, activeRegion}).iterator();
}
