Function removeRepeats

MergePaths/MergePaths.cpp:222–255

Remove tandem repeats from the set of paths. * @return the removed paths */

 * @return the removed paths
 */
static set<ContigID>
removeRepeats(ContigPathMap& paths)
{
	set<ContigID> repeats = findRepeats(paths);
	if (gDebugPrint) {
		cout << "Repeats:";
		if (!repeats.empty()) {
			for (set<ContigID>::const_iterator it = repeats.begin(); it != repeats.end(); ++it)
				cout << ' ' << get(g_contigNames, *it);
		} else
			cout << " none";
		cout << '\n';
	}

	unsigned removed = 0;
	for (set<ContigID>::const_iterator it = repeats.begin(); it != repeats.end(); ++it)
		if (paths.count(*it) > 0)
			removed++;
	if (removed == paths.size()) {
		// Every path was identified as a repeat. It's most likely a
		// cyclic sequence. Don't remove anything.
		repeats.clear();
		return repeats;
	}

	ostringstream ss;
	for (set<ContigID>::const_iterator it = repeats.begin(); it != repeats.end(); ++it)
		if (paths.erase(*it) > 0)
			ss << ' ' << get(g_contigNames, *it);

	if (opt::verbose > 0 && removed > 0)
		cout << "Removing paths in repeats:" << ss.str() << '\n';
	return repeats;
}

static void
appendToMergeQ(deque<ContigNode>& mergeQ, set<ContigNode>& seen, const ContigPath& path)