Function addPathOverlapEdges

PathOverlap/PathOverlap.cpp:427–464

Add the path overlap edges to the specified graph. */

/** Add the path overlap edges to the specified graph. */
static void
addPathOverlapEdges(
    Graph& g,
    const Paths& paths,
    const vector<string>& pathIDs,
    const Overlaps& overlaps)
{
	typedef graph_traits<Graph>::vertex_descriptor V;
	const bool allowParallelEdge = opt::mode == opt::ASSEMBLE;

	// Add the path vertices.
	g_contigNames.unlock();
	for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it) {
		const ContigPath& path = *it;
		const string& id = pathIDs[it - paths.begin()];
		if (!path.empty()) {
			V u = merge(g, path.begin(), path.end());
			put(vertex_name, g, u, id);
		}
	}
	g_contigNames.lock();

	// Remove the single-end contigs that are in paths.
	for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it)
		remove_vertex_if(
		    g, it->begin(), it->end(), [](const ContigNode& c) { return !c.ambiguous(); });

	// Add the path edges.
	for (Overlaps::const_iterator it = overlaps.begin(); it != overlaps.end(); ++it) {
		V u = it->source.descriptor();
		V v = it->target.descriptor();
		if (allowParallelEdge || !edge(u, v, g).second)
			add_edge(u, v, it->distance, static_cast<DG&>(g));
		else if (opt::verbose > 0)
			cerr << "ambiguous overlap: " << get(vertex_name, g, u) << " -> "
			     << get(vertex_name, g, v) << '\n';
	}
}

typedef graph_traits<Graph>::edge_descriptor edge_descriptor;