C++ ContigNode::sense方法代码示例

/** Attempt to merge the paths specified in mergeQ with path.
 * @return the number of paths merged
 */
static unsigned mergePaths(const Lengths& lengths,
		ContigPath& path,
		deque<ContigNode>& mergeQ, set<ContigNode>& seen,
		const ContigPathMap& paths)
{
	unsigned merged = 0;
	deque<ContigNode> invalid;
	for (ContigNode pivot; !mergeQ.empty(); mergeQ.pop_front()) {
		pivot = mergeQ.front();
		ContigPathMap::const_iterator path2It
			= paths.find(pivot.contigIndex());
		if (path2It == paths.end())
			continue;

		ContigPath path2 = path2It->second;
		if (pivot.sense())
			reverseComplement(path2.begin(), path2.end());
		ContigPath consensus = align(lengths, path, path2, pivot);
		if (consensus.empty()) {
			invalid.push_back(pivot);
			continue;
		}

		appendToMergeQ(mergeQ, seen, path2);
		path.swap(consensus);
		if (gDebugPrint)
#pragma omp critical(cout)
			cout << get(g_contigNames, pivot)
				<< '\t' << path2 << '\n'
				<< '\t' << path << '\n';
		merged++;
	}
	mergeQ.swap(invalid);
	return merged;
}

static void writeEstimate(ostream& out,
		const ContigNode& id0, const ContigNode& id1,
		unsigned len0, unsigned len1,
		const Pairs& pairs, const PMF& pmf)
{
	if (pairs.size() < opt::npairs)
		return;

	DistanceEst est;
	est.distance = estimateDistance(len0, len1,
			pairs, pmf, est.numPairs);
	est.stdDev = pmf.getSampleStdDev(est.numPairs);

	std::pair<ContigNode, ContigNode> e(id0, id1 ^ id0.sense());
	if (est.numPairs >= opt::npairs) {
		if (opt::format == DOT) {
#pragma omp critical(out)
			out << get(g_contigNames, e) << " [" << est << "]\n";
		} else
			out << ' ' << get(g_contigNames, id1) << ',' << est;
	} else if (opt::verbose > 1) {
#pragma omp critical(cerr)
		cerr << "warning: " << get(g_contigNames, e)
			<< " [d=" << est.distance << "] "
			<< est.numPairs << " of " << pairs.size()
			<< " pairs fit the expected distribution\n";
	}
}

/** Return a path, complemented if necessary. */
static ContigPath getPath(const Paths& paths, const ContigNode& u)
{
	if (isPath(u)) {
		unsigned i = u.id() - Vertex::s_offset;
		return u.sense() ? reverseComplement(paths[i]) : paths[i];
	} else
		return ContigPath(1, u);
}

/** Return the specified path. */
static ContigPath getPath(const ContigPathMap& paths, ContigNode u)
{
	ContigPathMap::const_iterator it = paths.find(u.contigIndex());
	assert(it != paths.end());
	ContigPath path = it->second;
	if (u.sense())
		reverseComplement(path.begin(), path.end());
	return path;
}

/** Return the sequence of the specified contig node. The sequence
 * may be ambiguous or reverse complemented.
 */
static Sequence sequence(const Contigs& contigs, const ContigNode& id)
{
	if (id.ambiguous()) {
		string s(id.ambiguousSequence());
		if (s.length() < opt::k)
			transform(s.begin(), s.end(), s.begin(), ::tolower);
		return string(opt::k - 1, 'N') + s;
	} else {
		const Sequence& seq = contigs[id.id()].seq;
		return id.sense() ? reverseComplement(seq) : seq;
	}
}

/** Return the sequence of the specified contig node. The sequence
 * may be ambiguous or reverse complemented.
 */
static const Sequence getSequence(ContigNode id)
{
	if (id.ambiguous()) {
		string s(id.ambiguousSequence());
		if (s.length() < opt::k)
			transform(s.begin(), s.end(), s.begin(), ::tolower);
		return string(opt::k - 1, 'N') + s;
	} else {
		string seq(g_contigs[id.id()]);
		return id.sense() ? reverseComplement(seq) : seq;
	}
}

/** Add the overlaps of vseq to the graph. */
static void addOverlapsSA(Graph& g, const SuffixArray& sa,
		ContigNode v, const string& vseq)
{
	assert(!vseq.empty());
	set<ContigNode> seen;
	typedef SuffixArray::const_iterator It;
	for (string q(vseq, 0, vseq.size() - 1);
			q.size() >= opt::minOverlap; chop(q)) {
		pair<It, It> range = sa.equal_range(q);
		for (It it = range.first; it != range.second; ++it) {
			ContigNode u(it->second);
			if (opt::ss && u.sense() != v.sense())
				continue;
			if (seen.insert(u).second) {
				// Add the longest overlap between two vertices.
				unsigned overlap = it->first.size();
				add_edge(u, v, -overlap, static_cast<DG&>(g));
			}
		}
	}
}

/** Return the sequence of the specified contig. */
static string sequence(const ContigNode& id)
{
	const string& seq = g_contigs[id.id()];
	return id.sense() ? reverseComplement(seq) : seq;
}

/** Identify paths subsumed by the specified path.
 * @param overlaps [out] paths that are found to overlap
 * @return the ID of the subsuming path
 */
static ContigID identifySubsumedPaths(const Lengths& lengths,
		ContigPathMap::const_iterator path1It,
		ContigPathMap& paths,
		set<ContigID>& out,
		set<ContigID>& overlaps)
{
	ostringstream vout;
	out.clear();
	ContigID id(path1It->first);
	const ContigPath& path = path1It->second;
	if (gDebugPrint)
		vout << get(g_contigNames, ContigNode(id, false))
			<< '\t' << path << '\n';

	for (ContigPath::const_iterator it = path.begin();
			it != path.end(); ++it) {
		ContigNode pivot = *it;
		if (pivot.ambiguous() || pivot.id() == id)
			continue;
		ContigPathMap::iterator path2It
			= paths.find(pivot.contigIndex());
		if (path2It == paths.end())
			continue;
		ContigPath path2 = path2It->second;
		if (pivot.sense())
			reverseComplement(path2.begin(), path2.end());
		ContigPath consensus = align(lengths, path, path2, pivot);
		if (consensus.empty())
			continue;
		if (equalIgnoreAmbiguos(consensus, path)) {
			if (gDebugPrint)
				vout << get(g_contigNames, pivot)
					<< '\t' << path2 << '\n';
			out.insert(path2It->first);
		} else if (equalIgnoreAmbiguos(consensus, path2)) {
			// This path is larger. Use it as the seed.
			return identifySubsumedPaths(lengths, path2It, paths, out,
					overlaps);
		} else if (isCycle(lengths, consensus)) {
			// The consensus path is a cycle.
			bool isCyclePath1 = isCycle(lengths, path);
			bool isCyclePath2 = isCycle(lengths, path2);
			if (!isCyclePath1 && !isCyclePath2) {
				// Neither path is a cycle.
				if (gDebugPrint)
					vout << get(g_contigNames, pivot)
						<< '\t' << path2 << '\n'
						<< "ignored\t" << consensus << '\n';
				overlaps.insert(id);
				overlaps.insert(path2It->first);
			} else {
				// At least one path is a cycle.
				if (gDebugPrint)
					vout << get(g_contigNames, pivot)
						<< '\t' << path2 << '\n'
						<< "cycle\t" << consensus << '\n';
				if (isCyclePath1 && isCyclePath2)
					out.insert(path2It->first);
				else if (!isCyclePath1)
					overlaps.insert(id);
				else if (!isCyclePath2)
					overlaps.insert(path2It->first);
			}
		} else {
			if (gDebugPrint)
				vout << get(g_contigNames, pivot)
					<< '\t' << path2 << '\n'
					<< "ignored\t" << consensus << '\n';
			overlaps.insert(id);
			overlaps.insert(path2It->first);
		}
	}
	cout << vout.str();
	return id;
}