else if (!graphLikelihoodEngine.hasVariation())
logger.debug("Resulting haplotype graph does not contain any alternative haplotype path");
if (debugMode == DebugMode.EXTRA_DEBUG) {
graphLikelihoodEngine.printGraph(originalActiveRegion.getLocation() + "-" + graphLikelihoodEngine.getKmerSize() + "-haplotypeGraph.dot");
final SeqGraph sq = graphLikelihoodEngine.haplotypeGraph.convertToSequenceGraph();
sq.simplifyGraph();
sq.printGraph(new File(originalActiveRegion.getLocation() + "-" + graphLikelihoodEngine.getKmerSize() + "-haplotypeSeqGraph.dot"), 10000);
try {
final FileWriter fw = new FileWriter(new File(originalActiveRegion.getLocation() + "-likelihoods.txt"));
final PrintWriter pw = new PrintWriter(fw);
//Note: we only output the first sample likelihoods, perhaps should output all of them but for debugging this is normally what is needed.