Function readPaths

PathOverlap/PathOverlap.cpp:221–251

Read contig paths from the specified file. * @param g the contig adjacency graph * @param inPath the file of contig paths * @param[out] pathIDs the path IDs * @return the paths */

 * @return the paths
 */
static Paths
readPaths(Graph& g, const string& inPath, vector<string>& pathIDs)
{
	typedef graph_traits<Graph>::vertex_descriptor V;

	assert(pathIDs.empty());
	ifstream fin(inPath.c_str());
	if (opt::verbose > 0)
		cerr << "Reading `" << inPath << "'..." << endl;
	if (inPath != "-")
		assert_good(fin, inPath);
	istream& in = inPath == "-" ? cin : fin;

	assert_good(in, inPath);
	Paths paths;
	string id;
	ContigPath path;
	while (in >> id >> path) {
		if (path.empty()) {
			// Remove this contig from the graph.
			V u = find_vertex(id, false, g);
			clear_vertex(u, g);
			remove_vertex(u, g);
		} else {
			pathIDs.push_back(id);
			paths.push_back(path);
		}
	}
	assert(in.eof());
	return paths;
}

typedef multimap<ContigNode, Vertex> SeedMap;