Function buildPathGraph

MergePaths/MergePaths.cpp:845–886

Build the path overlap graph. */

/** Build the path overlap graph. */
static void
buildPathGraph(const Lengths& lengths, PathGraph& g, const ContigPathMap& paths)
{
	// Create the vertices of the path overlap graph.
	PathGraph(lengths.size()).swap(g);

	// Remove the non-seed contigs.
	typedef graph_traits<PathGraph>::vertex_iterator vertex_iterator;
	pair<vertex_iterator, vertex_iterator> vit = g.vertices();
	for (vertex_iterator u = vit.first; u != vit.second; ++u)
		if (paths.count(get(vertex_contig_index, g, *u)) == 0)
			remove_vertex(*u, g);

	// Find the overlapping paths.
	ContigPathMap::const_iterator sharedIt = paths.begin();
#pragma omp parallel
	for (ContigPathMap::const_iterator it; atomicInc(sharedIt, paths.end(), it);)
		findPathOverlaps(lengths, paths, ContigNode(it->first, false), it->second, g);
	if (gDebugPrint)
		cout << '\n';

	addMissingEdges(lengths, g, paths);
	removeTransitiveEdges(g);
	removeSmallOverlaps(g, paths);
	if (opt::verbose > 0)
		printGraphStats(cout, g);

	// graph statistics
	vector<int> vals = passGraphStatsVal(g);
	vector<string> keys = make_vector<string>() << "V"
	                                            << "E"
	                                            << "degree0pctg"
	                                            << "degree1pctg"
	                                            << "degree234pctg"
	                                            << "degree5pctg"
	                                            << "degree_max";
	if (!opt::db.empty()) {
		for (unsigned i = 0; i < vals.size(); i++)
			addToDb(db, keys[i], vals[i]);
	}
	outputPathGraph(g);
}

/** Read contig lengths. */
static Lengths