/// Compute total number of edges static size_t computeNumberOfEdges(const Paths& paths) { size_t count=0; for (Paths::const_iterator i = paths.begin(), e = paths.end(); i != e; ++i) { count += i->size(); } return count; }
int main(int argc, char** argv) { string commandLine; { ostringstream ss; char** last = argv + argc - 1; copy(argv, last, ostream_iterator<const char *>(ss, " ")); ss << *last; commandLine = ss.str(); } if (!opt::db.empty()) opt::metaVars.resize(3); bool die = false; for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) { istringstream arg(optarg != NULL ? optarg : ""); switch (c) { case '?': die = true; break; case 'g': arg >> opt::graphPath; break; case 'k': arg >> opt::k; break; case 'r': arg >> opt::repeatContigs; break; case 'v': opt::verbose++; break; case OPT_HELP: cout << USAGE_MESSAGE; exit(EXIT_SUCCESS); case OPT_VERSION: cout << VERSION_MESSAGE; exit(EXIT_SUCCESS); case OPT_DB: arg >> opt::db; break; case OPT_LIBRARY: arg >> opt::metaVars[0]; break; case OPT_STRAIN: arg >> opt::metaVars[1]; break; case OPT_SPECIES: arg >> opt::metaVars[2]; break; } if (optarg != NULL && !arg.eof()) { cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n"; exit(EXIT_FAILURE); } } if (opt::k <= 0) { cerr << PROGRAM ": missing -k,--kmer option\n"; die = true; } if (argc - optind < 2) { cerr << PROGRAM ": missing arguments\n"; die = true; } else if (argc - optind > 2) { cerr << PROGRAM ": too many arguments\n"; die = true; } if (die) { cerr << "Try `" << PROGRAM << " --help' for more information.\n"; exit(EXIT_FAILURE); } const char *adjPath = argv[optind++]; if (opt::verbose > 0) cerr << "Reading `" << adjPath << "'..." << endl; ifstream fin(adjPath); assert_good(fin, adjPath); Graph g; fin >> g; Vertex::s_offset = g.num_vertices() / 2; string pathsFile(argv[optind++]); vector<string> pathIDs; Paths paths = readPaths(g, pathsFile, pathIDs); switch (opt::mode) { case opt::OVERLAP: // Find overlapping paths, do not assemble. addPathOverlapEdges(g, paths, pathIDs, findOverlaps(g, paths)); paths.clear(); if (opt::graphPath.empty()) opt::graphPath = "-"; break; case opt::ASSEMBLE: // Assemble overlapping paths. assembleOverlappingPaths(g, paths, pathIDs); break; case opt::TRIM: // Trim overlapping paths. trimOverlaps(g, paths); // Remove paths consisting of a single contig. for_each_if(paths.begin(), paths.end(), mem_fun_ref(&ContigPath::clear), compose1( bind2nd(equal_to<ContigPath::size_type>(), 1), mem_fun_ref(&ContigPath::size))); // Add the paths to the graph. addPathOverlapEdges(g, paths, pathIDs, Overlaps()); break; } // Output the paths. for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it) { if (it->empty()) continue; assert(it->size() != 1); cout << pathIDs[it - paths.begin()] << '\t' << *it << '\n'; } assert(cout.good()); // Output the graph. if (!opt::graphPath.empty()) { ofstream fout; ostream& out = opt::graphPath == "-" ? cout : (fout.open(opt::graphPath.c_str()), fout); assert_good(out, opt::graphPath); write_graph(out, g, PROGRAM, commandLine); assert_good(out, opt::graphPath); } // Output the repeat contigs. if (!opt::repeatContigs.empty()) { sort(s_trimmedContigs.begin(), s_trimmedContigs.end()); s_trimmedContigs.erase( unique(s_trimmedContigs.begin(), s_trimmedContigs.end()), s_trimmedContigs.end()); ofstream out(opt::repeatContigs.c_str()); assert_good(out, opt::repeatContigs); for (vector<ContigID>::const_iterator it = s_trimmedContigs.begin(); it != s_trimmedContigs.end(); ++it) out << get(g_contigNames, *it) << '\n'; assert_good(out, opt::repeatContigs); } if (!opt::db.empty()) { init(db, opt::db, opt::verbose, PROGRAM, opt::getCommand(argc, argv), opt::metaVars); addToDb(db, "SS", opt::ss); addToDb(db, "K", opt::k); } return 0; }