Beispiel #1
0
/** Record the trimmed contigs. */
static void recordTrimmedContigs(
		ContigPath::const_iterator first,
		ContigPath::const_iterator last)
{
	for (ContigPath::const_iterator it = first; it != last; ++it)
		if (!it->ambiguous())
			s_trimmedContigs.push_back(it->contigIndex());
}
Beispiel #2
0
/** Return the set of contigs that appear more than once in a single
 * solution.
 */
static set<ContigID> findRepeats(ContigID seed,
	const ContigPaths& solutions)
{
	set<ContigID> repeats;
	for (ContigPaths::const_iterator solIt = solutions.begin();
			solIt != solutions.end(); ++solIt) {
		map<ContigID, unsigned> count;
		count[seed]++;
		for (ContigPath::const_iterator it = solIt->begin();
				it != solIt->end(); ++it)
			count[it->contigIndex()]++;
		for (map<ContigID, unsigned>::const_iterator
				it = count.begin(); it != count.end(); ++it)
			if (it->second > 1)
				repeats.insert(it->first);
	}
	return repeats;
}
/** Return all contigs that are tandem repeats, identified as those
 * contigs that appear more than once in a single path.
 */
static set<ContigID> findRepeats(const ContigPathMap& paths)
{
	set<ContigID> repeats;
	for (ContigPathMap::const_iterator pathIt = paths.begin();
			pathIt != paths.end(); ++pathIt) {
		const ContigPath& path = pathIt->second;
		map<ContigID, unsigned> count;
		for (ContigPath::const_iterator it = path.begin();
				it != path.end(); ++it)
			if (!it->ambiguous())
				count[it->contigIndex()]++;
		for (map<ContigID, unsigned>::const_iterator
				it = count.begin(); it != count.end(); ++it)
			if (it->second > 1)
				repeats.insert(it->first);
	}
	return repeats;
}