Function removeContigs

FilterGraph/FilterGraph.cc:349–382

Remove the specified contig from the adjacency graph. */

/** Remove the specified contig from the adjacency graph. */
static void
removeContigs(Graph& g, vector<vertex_descriptor>& sc)
{
	typedef graph_traits<Graph> GTraits;
	typedef GTraits::vertex_descriptor V;

	vector<vertex_descriptor> out;
	out.reserve(sc.size());

	vector<bool> markedContigs(g.num_vertices());
	for (vector<vertex_descriptor>::iterator it = sc.begin(); it != sc.end(); ++it) {
		V v = *it;
		if (opt::verbose > 0 && ++g_count.checked % 10000000 == 0)
			cerr << "Removed " << g_count.removed << "/" << g_count.checked
			     << " vertices that have been checked.\n";

		if (markedContigs[get(vertex_index, g, v)]) {
			out.push_back(v);
			continue;
		}

		if (!removable(&g, v))
			continue;

		vector<EdgeInfo> eds;
		if (findNewEdges(g, v, eds, markedContigs))
			addNewEdges(g, eds);
		else
			continue;

		removeContig(v, g);
	}
	sc.swap(out);
}

/** Return the value of the bit at the specified index. */
struct Marked