Function assembleContigs

RResolver/Contigs.cpp:195–258

}

void
assembleContigs()
{
	if (opt::verbose) {
		std::cerr << "Assembling contigs... ";
	}

	std::vector<std::string> pathIDs;
	ContigPaths paths;

	Graph newContigGraph(g_contigGraph);
	assemble(newContigGraph, back_inserter(paths));
	assert(num_vertices(newContigGraph) >= num_vertices(g_contigGraph));

	// Record all the contigs that are in a path.
	std::vector<bool> seen(g_contigGraph.num_vertices() / 2);

	g_contigNames.unlock();
	int counter = 0;
	for (const auto& path : paths) {
		assert(!path.empty());
		ContigNode pathNode(g_contigGraph.num_vertices() / 2 + counter, path[0].sense());
		std::string name = createContigName();
		pathIDs.push_back(name);
		put(vertex_name, newContigGraph, pathNode, name);
		for (const auto& node : path) {
			seen[node.id()] = true;
		}
		counter++;
	}
	g_contigNames.lock();

	for (const auto& path : paths) {
		assert(!path.empty());
		Sequence sequence = getPathSequence(path);
		unsigned coverage = 0;
		for (const auto& node : path) {
			if (!node.ambiguous()) {
				coverage += g_contigGraph[node].coverage;
			}
		}

		std::stringstream ss;
		ss << sequence.size() << ' ' << coverage << ' ';
		ss << get(vertex_name, g_contigGraph, path.front());
		if (path.size() == 1)
			return;
		else if (path.size() == 3)
			ss << ',' << get(vertex_name, g_contigGraph, path[1]);
		else if (path.size() > 3)
			ss << ",...";
		ss << ',' << get(vertex_name, g_contigGraph, path.back());

		g_contigSequences.push_back(sequence);
		g_contigSequences.push_back(reverseComplement(sequence));
		g_contigComments.push_back(ss.str());
	}