final Cigar c = new Cigar();
c.add(new CigarElement(refHaplotype.getBases().length, CigarOperator.M));
refHaplotype.setCigar(c);
final ActiveRegion activeRegion = new ActiveRegion(loc, null, true, genomeLocParser, 0);
activeRegion.addAll(reads);
// logger.warn("Assembling " + activeRegion + " with " + engine);
final AssemblyResultSet assemblyResultSet = assembler.runLocalAssembly(activeRegion, refHaplotype, refBases, loc, Collections.<VariantContext>emptyList(), null);
return assemblyResultSet.getHaplotypeList();
}