Beispiel #1
0
/** 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));

		}
	}
}
Beispiel #2
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());
}
static void appendToMergeQ(deque<ContigNode>& mergeQ,
	set<ContigNode>& seen, const ContigPath& path)
{
	for (ContigPath::const_iterator it = path.begin();
			it != path.end(); ++it)
		if (!it->ambiguous() && seen.insert(*it).second)
			mergeQ.push_back(*it);
}
Beispiel #4
0
/** Finds all contigs used in each path in paths, and
 * marks them as seen in the vector seen. */
static void seenContigs(vector<bool>& seen, const ContigPaths& paths)
{
	for (ContigPaths::const_iterator it = paths.begin();
			it != paths.end(); ++it)
		for (ContigPath::const_iterator itc = it->begin();
				itc != it->end(); ++itc)
			if (itc->id() < seen.size())
				seen[itc->id()] = true;
}
/** Return a pivot suitable for aligning the two paths if one exists,
 * otherwise return false.
 */
static pair<ContigNode, bool> findPivot(
		const ContigPath& path1, const ContigPath& path2)
{
	for (ContigPath::const_iterator it = path2.begin();
			it != path2.end(); ++it) {
		if (it->ambiguous())
			continue;
		if (count(path2.begin(), path2.end(), *it) == 1
				&& count(path1.begin(), path1.end(), *it) == 1)
			return make_pair(*it, true);
	}
	return make_pair(ContigNode(0), false);
}
Beispiel #6
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;
}
Beispiel #8
0
/** Merge the specified path. */
static Contig mergePath(const Graph& g, const Contigs& contigs,
		const ContigPath& path)
{
	Sequence seq;
	unsigned coverage = 0;
	for (ContigPath::const_iterator it = path.begin();
			it != path.end(); ++it) {
		if (!it->ambiguous())
			coverage += g[*it].coverage;
		if (seq.empty()) {
			seq = sequence(contigs, *it);
		} else {
			assert(it != path.begin());
			mergeContigs(g, contigs, *(it-1), *it, seq, path);
		}
	}
	ostringstream ss;
	ss << seq.size() << ' ' << coverage << ' ';
	pathToComment(ss, g, path);
	return Contig(ss.str(), seq);
}