Function assembleOverlappingPaths

PathOverlap/PathOverlap.cpp:535–575

Assemble overlapping paths. */

/** Assemble overlapping paths. */
static void
assembleOverlappingPaths(Graph& g, Paths& paths, vector<string>& pathIDs)
{
	if (paths.empty())
		return;

	// Find overlapping paths.
	Overlaps overlaps = findOverlaps(g, paths);
	addPathOverlapEdges(g, paths, pathIDs, overlaps);

	// Create a property map of path overlaps.
	OverlapMap overlapMap;
	for (Overlaps::const_iterator it = overlaps.begin(); it != overlaps.end(); ++it)
		overlapMap.insert(OverlapMap::value_type(
		    OverlapMap::key_type(it->source.descriptor(), it->target.descriptor()), it->overlap));

	// Assemble unambiguously overlapping paths.
	Paths merges;
	assemble_if(g, back_inserter(merges), IsPathOverlap(g, overlapMap, IsPositive<Graph>(g)));

	// Merge overlapping paths.
	g_contigNames.unlock();
	assert(!pathIDs.empty());
	setNextContigName(pathIDs.back());
	for (Paths::const_iterator it = merges.begin(); it != merges.end(); ++it) {
		string name = createContigName();
		if (opt::verbose > 0)
			cerr << name << '\t' << *it << '\n';
		Vertex u(paths.size(), false);
		put(vertex_name, g, u.descriptor(), name);
		pathIDs.push_back(name);
		paths.push_back(mergePaths(paths, overlapMap, *it));

		// Remove the merged paths.
		for (ContigPath::const_iterator it2 = it->begin(); it2 != it->end(); ++it2) {
			if (isPath(*it2))
				paths[it2->id() - Vertex::s_offset].clear();
		}
	}
	g_contigNames.lock();
}

int
main(int argc, char** argv)