Function removeSmallOverlaps

MergePaths/MergePaths.cpp:692–724

Remove ambiguous edges that overlap by only a small amount. * Remove the edge (u,v) if deg+(u) > 1 and deg-(v) > 1 and the * overlap of (u,v) is small. */

 * overlap of (u,v) is small.
 */
static void
removeSmallOverlaps(PathGraph& g, const ContigPathMap& paths)
{
	typedef graph_traits<PathGraph>::edge_descriptor E;
	typedef graph_traits<PathGraph>::out_edge_iterator Eit;
	typedef graph_traits<PathGraph>::vertex_descriptor V;
	typedef graph_traits<PathGraph>::vertex_iterator Vit;

	vector<E> edges;
	pair<Vit, Vit> urange = vertices(g);
	for (Vit uit = urange.first; uit != urange.second; ++uit) {
		V u = *uit;
		if (out_degree(u, g) < 2)
			continue;
		ContigPath pathu = getPath(paths, u);
		pair<Eit, Eit> uvits = out_edges(u, g);
		for (Eit uvit = uvits.first; uvit != uvits.second; ++uvit) {
			E uv = *uvit;
			V v = target(uv, g);
			assert(v != u);
			if (in_degree(v, g) < 2)
				continue;
			ContigPath pathv = getPath(paths, v);
			if (pathu.back() == pathv.front() && paths.count(pathu.back().contigIndex()) > 0)
				edges.push_back(uv);
		}
	}
	remove_edges(g, edges.begin(), edges.end());
	if (opt::verbose > 0)
		cout << "Removed " << edges.size() << " small overlap edges.\n";
	if (!opt::db.empty())
		addToDb(db, "Edges_removed_small_overlap", edges.size());
}

/** Output the path overlap graph. */
static void