Function buildOverlapGraph

AdjList/AdjList.cpp:242–270

/** Build contig overlap graph. */
template <class KmerType>
static void buildOverlapGraph(Graph& g, vector<KmerType>& prefixes,
	unordered_map<KmerType, vector<ContigNode> >& suffixMap)
{
	// Add the overlap edges of exactly k-1 bp.

	typedef graph_traits<Graph>::vertex_descriptor V;
	typedef unordered_map<KmerType, vector<ContigNode> > SuffixMap;
	typedef typename vector<KmerType>::const_iterator PrefixIterator;
	typedef const typename SuffixMap::mapped_type Edges;
	typedef typename SuffixMap::mapped_type::const_iterator SuffixIterator;

	if (opt::verbose > 0)
		cerr << "Finding overlaps of exactly k-1 bp...\n";
	for (PrefixIterator it = prefixes.begin(); it != prefixes.end(); ++it) {
		ContigNode v(it - prefixes.begin());
		Edges& edges = suffixMap[*it];
		for (SuffixIterator itu = edges.begin(); itu != edges.end(); ++itu) {
			V uc = get(vertex_complement, g, *itu);
			V vc = get(vertex_complement, g, v);
			if (opt::ss && uc.sense() != vc.sense())
				continue;
			add_edge(vc, uc, -(int)opt::k + 1, static_cast<DG&>(g));
		}
	}
	SuffixMap().swap(suffixMap);

	if (opt::verbose > 0)
		printGraphStats(cerr, g);
}

template <class KmerType>
void loadDataStructures(Graph& g, vector<KmerType>& prefixes,