Function assemblePathGraph

MergePaths/MergePaths.cpp:764–796

Assemble the path overlap graph. */

/** Assemble the path overlap graph. */
static void
assemblePathGraph(const Lengths& lengths, PathGraph& pathGraph, ContigPathMap& paths)
{
	ContigPaths seedPaths;
	assembleDFS(pathGraph, back_inserter(seedPaths));
	ContigPaths mergedPaths = mergeSeedPaths(lengths, paths, seedPaths);
	if (opt::verbose > 1)
		cout << '\n';

	// Replace each path with the merged path.
	for (ContigPaths::const_iterator it1 = seedPaths.begin(); it1 != seedPaths.end(); ++it1) {
		const ContigPath& path(mergedPaths[it1 - seedPaths.begin()]);
		ContigPath pathrc(path);
		reverseComplement(pathrc.begin(), pathrc.end());
		for (ContigPath::const_iterator it2 = it1->begin(); it2 != it1->end(); ++it2) {
			ContigNode seed(*it2);
			if (find(path.begin(), path.end(), seed) != path.end()) {
				paths[seed.contigIndex()] = seed.sense() ? pathrc : path;
			} else {
				// This seed was not included in the merged path.
			}
		}
	}

	removeRepeats(paths);

	// Remove the subsumed paths.
	if (opt::verbose > 0)
		cout << "Removing redundant contigs\n";
	removeSubsumedPaths(lengths, paths);

	outputSortedPaths(lengths, paths);
}

/** Read a set of paths from the specified file. */
static ContigPathMap