Function findOverlaps

PathOverlap/PathOverlap.cpp:306–335

Find every path that overlaps with the specified path. */

/** Find every path that overlaps with the specified path. */
static void
findOverlaps(
    const Graph& g,
    const Paths& paths,
    const SeedMap& seedMap,
    const Vertex& v,
    Overlaps& overlaps)
{
	ContigPath rc;
	if (v.sense) {
		rc = paths[v.id];
		reverseComplement(rc.begin(), rc.end());
	}
	const ContigPath& path = v.sense ? rc : paths[v.id];

	for (ContigPath::const_iterator it = path.begin(); it != path.end(); ++it) {
		if (it->ambiguous())
			continue;

		pair<SeedMap::const_iterator, SeedMap::const_iterator> range = seedMap.equal_range(*it);
		for (SeedMap::const_iterator seed = range.first; seed != range.second; ++seed) {
			if (v == seed->second)
				continue;
			int distance = 0;
			unsigned overlap = findOverlap(g, paths, it, path.end(), seed->second, distance);
			if (overlap > 0)
				overlaps.push_back(Overlap(v, seed->second, overlap, distance));
		}
	}
}

/** Find every pair of overlapping paths. */
static Overlaps