int main(int argc, char *argv[]) { CLParserPtr optParser = initParser(); string inPath, deleteNode; bool noMarkAncestors; try { optParser->parseOptions(argc, argv); inPath = optParser->getArgument<string>("inFile"); deleteNode = optParser->getArgument<string>("deleteNode"); noMarkAncestors = optParser->getFlag("noMarkAncestors"); } catch (exception &e) { optParser->printUsage(cerr); return 1; } AlignmentPtr alignment = openHalAlignment(inPath, optParser); if (!noMarkAncestors) { markAncestorsForUpdate(alignment, deleteNode); } alignment->removeGenome(deleteNode); return 0; }