final int length = activeRegion.getExtendedLoc().size();
final RandomDNA rnd = new RandomDNA(13); // keep it prepoducible by fixing the seed to lucky 13.
final ActiveRegionTestDataSet actd = new ActiveRegionTestDataSet(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.getExtendedLoc());
final ReadThreadingGraph rtg = new ReadThreadingGraph(10);
for (final Haplotype h : haplotypes)