@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();
}
@DataProvider(name = "assemblyResults")
public java.util.Iterator<Object[]> assemblyResults() {
final int size =
THREE_KS_GRAPH_AND_HAPLOTYPES.length * (1 + TEN_KS_GRAPH_AND_HAPLOTYPES.length);
final Object[][] result = new Object[size][];
for (int i = 0; i < THREE_KS_GRAPH_AND_HAPLOTYPES.length; i++) {
final ReadThreadingGraph rtg =
new TestingReadThreadingGraph((String) THREE_KS_GRAPH_AND_HAPLOTYPES[i][0]);
final AssemblyResult ar =
new AssemblyResult(
AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, rtg.toSequenceGraph(), rtg);
final Object[] haplotypeStrings = (Object[]) THREE_KS_GRAPH_AND_HAPLOTYPES[i][1];
final Haplotype[] haplotypes = new Haplotype[haplotypeStrings.length];
for (int j = 0; j < haplotypeStrings.length; j++) {
haplotypes[j] = new Haplotype(((String) haplotypeStrings[j]).getBytes(), j == 0);
haplotypes[j].setGenomeLocation(
genomeLocParser.createGenomeLoc("1", 1, haplotypes[j].length() + 1));
}
result[i] =
new Object[] {Collections.singletonList(ar), Arrays.asList(Arrays.asList(haplotypes))};
for (int j = 0; j < TEN_KS_GRAPH_AND_HAPLOTYPES.length; j++) {
final ReadThreadingGraph rtg10 =
new TestingReadThreadingGraph((String) TEN_KS_GRAPH_AND_HAPLOTYPES[j][0]);
final AssemblyResult ar10 =
new AssemblyResult(
AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, rtg10.toSequenceGraph(), rtg10);
final Object[] haplotypeStrings10 = (Object[]) TEN_KS_GRAPH_AND_HAPLOTYPES[j][1];
final Haplotype[] haplotype10 = new Haplotype[haplotypeStrings10.length];
for (int k = 0; k < haplotypeStrings10.length; k++) {
haplotype10[k] = new Haplotype(((String) haplotypeStrings10[k]).getBytes(), false);
haplotype10[k].setGenomeLocation(
genomeLocParser.createGenomeLoc("1", 1, haplotype10[k].length() + 1));
}
result[THREE_KS_GRAPH_AND_HAPLOTYPES.length + i * TEN_KS_GRAPH_AND_HAPLOTYPES.length + j] =
new Object[] {
Arrays.asList(ar, ar10),
Arrays.asList(Arrays.asList(haplotypes), Arrays.asList(haplotype10))
};
}
}
return Arrays.asList(result).iterator();
}
@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);
}