C++ ContigPath::end方法代码示例

/** Add an edge if the two paths overlap.
 * @param pivot the pivot at which to seed the alignment
 * @return whether an overlap was found
 */
static bool addOverlapEdge(const Lengths& lengths,
		PathGraph& gout, ContigNode pivot,
		ContigNode seed1, const ContigPath& path1,
		ContigNode seed2, const ContigPath& path2)
{
	assert(seed1 != seed2);

	// Determine the orientation of the overlap edge.
	dir_type orientation = DIR_X;
	ContigPath consensus = align(lengths,
			path1, path2, pivot, orientation);
	if (consensus.empty())
		return false;
	assert(orientation != DIR_X);
	if (orientation == DIR_B) {
		// One of the paths subsumes the other. Use the order of the
		// seeds to determine the orientation of the edge.
		orientation = find(consensus.begin(), consensus.end(), seed1)
			< find(consensus.begin(), consensus.end(), seed2)
			? DIR_F : DIR_R;
	}
	assert(orientation == DIR_F || orientation == DIR_R);

	// Add the edge.
	ContigNode u = orientation == DIR_F ? seed1 : seed2;
	ContigNode v = orientation == DIR_F ? seed2 : seed1;
	bool added = false;
#pragma omp critical(gout)
	if (!edge(u, v, gout).second) {
		add_edge(u, v, gout);
		added = true;
	}
	return added;
}

/** Find an equivalent region of the two specified paths, starting the
 * alignment at pivot1 of path1 and pivot2 of path2.
 * @param[out] orientation the orientation of the alignment
 * @return the consensus sequence
 */
static ContigPath align(const Lengths& lengths,
		const ContigPath& p1, const ContigPath& p2,
		ContigPath::const_iterator pivot1,
		ContigPath::const_iterator pivot2,
		dir_type& orientation)
{
	assert(*pivot1 == *pivot2);
	ContigPath::const_reverse_iterator
		rit1 = ContigPath::const_reverse_iterator(pivot1+1),
		rit2 = ContigPath::const_reverse_iterator(pivot2+1);
	ContigPath alignmentr(p1.rend() - rit1 + p2.rend() - rit2);
	ContigPath::iterator rout = alignmentr.begin();
	dir_type alignedr = align(lengths,
			rit1, p1.rend(), rit2, p2.rend(), rout);
	alignmentr.erase(rout, alignmentr.end());

	ContigPath::const_iterator it1 = pivot1, it2 = pivot2;
	ContigPath alignmentf(p1.end() - it1 + p2.end() - it2);
	ContigPath::iterator fout = alignmentf.begin();
	dir_type alignedf = align(lengths,
			it1, p1.end(), it2, p2.end(), fout);
	alignmentf.erase(fout, alignmentf.end());

	ContigPath consensus;
	if (alignedr != DIR_X && alignedf != DIR_X) {
		// Found an alignment.
		assert(!alignmentf.empty());
		assert(!alignmentr.empty());
		consensus.reserve(alignmentr.size()-1 + alignmentf.size());
		consensus.assign(alignmentr.rbegin(), alignmentr.rend()-1);
		consensus.insert(consensus.end(),
				alignmentf.begin(), alignmentf.end());

		// Determine the orientation of the alignment.
		unsigned dirs = alignedr << 2 | alignedf;
		static const dir_type DIRS[16] = {
			DIR_X, // 0000 XX impossible
			DIR_X, // 0001 XF impossible
			DIR_X, // 0010 XR impossible
			DIR_X, // 0011 XB impossible
			DIR_X, // 0100 FX impossible
			DIR_B, // 0101 FF u is subsumed in v
			DIR_R, // 0110 FR v->u
			DIR_R, // 0111 FB v->u
			DIR_X, // 1000 RX impossible
			DIR_F, // 1001 RF u->v
			DIR_B, // 1010 RR v is subsumed in u
			DIR_F, // 1011 RB u->v
			DIR_X, // 1100 BX impossible
			DIR_F, // 1101 BF u->v
			DIR_R, // 1110 BR v->u
			DIR_B, // 1111 BB u and v are equal
		};
		assert(dirs < 16);
		orientation = DIRS[dirs];
		assert(orientation != DIR_X);
	}
	return consensus;
}

/** 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);
}

/** Remove ambiguous contigs from the ends of the path. */
static void removeAmbiguousContigs(ContigPath& path)
{
	if (!path.empty() && path.back().ambiguous())
		path.erase(path.end() - 1);
	if (!path.empty() && path.front().ambiguous())
		path.erase(path.begin());
}

/** 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));

		}
	}
}

/** Return a map of contig IDs to their distance along this path.
 * Repeat contigs, which would have more than one position, are not
 * represented in this map.
 */
map<ContigNode, int> makeDistanceMap(const Graph& g,
		const ContigNode& origin, const ContigPath& path)
{
	map<ContigNode, int> distances;
	int distance = 0;
	for (ContigPath::const_iterator it = path.begin();
			it != path.end(); ++it) {
		vertex_descriptor u = it == path.begin() ? origin : *(it - 1);
		vertex_descriptor v = *it;
		distance += getDistance(g, u, v);

		bool inserted = distances.insert(
				make_pair(v, distance)).second;
		if (!inserted) {
			// Mark this contig as a repeat.
			distances[v] = INT_MIN;
		}

		distance += g[v].length;
	}

	// Remove the repeats.
	for (map<ContigNode, int>::iterator it = distances.begin();
			it != distances.end();)
		if (it->second == INT_MIN)
			distances.erase(it++);
		else
			++it;
	return distances;
}

/** Remove the overlapping portion of the specified contig. */
static void removeContigs(ContigPath& path,
		unsigned first, unsigned last)
{
	assert(first <= path.size());
	assert(last <= path.size());
	if (first < last) {
		recordTrimmedContigs(path.begin(), path.begin() + first);
		recordTrimmedContigs(path.begin() + last, path.end());
		path.erase(path.begin() + last, path.end());
		path.erase(path.begin(), path.begin() + first);
	} else {
		recordTrimmedContigs(path.begin(), path.end());
		path.clear();
	}
	removeAmbiguousContigs(path);
}

/** Mark every contig in path as seen. */
static void markSeen(vector<bool>& seen, const ContigPath& path,
		bool flag)
{
	for (Path::const_iterator it = path.begin();
			it != path.end(); ++it)
		if (!it->ambiguous() && it->id() < seen.size())
			seen[it->id()] = flag;
}

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);
}

/** 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;
}

/** Check whether path starts with the sequence [first, last). */
static bool startsWith(ContigPath path, bool rc,
		ContigPath::const_iterator first,
		ContigPath::const_iterator last)
{
	if (rc)
		reverseComplement(path.begin(), path.end());
	assert(*first == path.front());
	assert(first < last);
	return unsigned(last - first) > path.size() ? false
		: equal(first, last, path.begin());
}

/** Merge the paths of the specified seed path.
 * @return the merged contig path
 */
static ContigPath mergePath(const Lengths& lengths,
		const ContigPathMap& paths, const ContigPath& seedPath)
{
	assert(!seedPath.empty());
	ContigNode seed1 = seedPath.front();
	ContigPathMap::const_iterator path1It
		= paths.find(seed1.contigIndex());
	assert(path1It != paths.end());
	ContigPath path(path1It->second);
	if (seedPath.front().sense())
		reverseComplement(path.begin(), path.end());
	if (opt::verbose > 1)
#pragma omp critical(cout)
		cout << "\n* " << seedPath << '\n'
			<< get(g_contigNames, seedPath.front())
			<< '\t' << path << '\n';
	for (ContigPath::const_iterator it = seedPath.begin() + 1;
			it != seedPath.end(); ++it) {
		ContigNode seed2 = *it;
		ContigPathMap::const_iterator path2It
			= paths.find(seed2.contigIndex());
		assert(path2It != paths.end());
		ContigPath path2 = path2It->second;
		if (seed2.sense())
			reverseComplement(path2.begin(), path2.end());

		ContigNode pivot
			= find(path.begin(), path.end(), seed2) != path.end()
			? seed2 : seed1;
		ContigPath consensus = align(lengths, path, path2, pivot);
		if (consensus.empty()) {
			// This seed could be removed from the seed path.
			if (opt::verbose > 1)
#pragma omp critical(cout)
				cout << get(g_contigNames, seed2)
					<< '\t' << path2 << '\n'
					<< "\tinvalid\n";
		} else {
			path.swap(consensus);
			if (opt::verbose > 1)
#pragma omp critical(cout)
				cout << get(g_contigNames, seed2)
					<< '\t' << path2 << '\n'
					<< '\t' << path << '\n';
		}
		seed1 = seed2;
	}
	return path;
}

/** Return the length of the specified path in k-mer. */
static unsigned calculatePathLength(const Graph& g,
		const ContigNode& origin,
		const ContigPath& path, size_t prefix = 0, size_t suffix = 0)
{
	if (prefix + suffix == path.size())
		return 0;
	assert(prefix + suffix < path.size());
	int length = addProp(g, path.begin() + prefix,
			path.end() - suffix).length;

	// Account for the overlap on the left.
	vertex_descriptor u = prefix == 0 ? origin : path[prefix - 1];
	length += getDistance(g, u, path[prefix]);
	assert(length > 0);
	return length;
}

/** Merge a sequence of overlapping paths. */
static ContigPath mergePaths(const Paths& paths,
		const OverlapMap& overlaps, const ContigPath& merge)
{
	assert(!merge.empty());
	ContigNode u = merge.front();
	ContigPath path(getPath(paths, u));
	for (ContigPath::const_iterator it = merge.begin() + 1;
			it != merge.end(); ++it) {
		ContigNode v = *it;
		ContigPath vpath(getPath(paths, v));
		unsigned overlap = getOverlap(overlaps, u, v);
		assert(path.size() > overlap);
		assert(vpath.size() > overlap);
		assert(equal(path.end() - overlap, path.end(),
					vpath.begin()));
		path.insert(path.end(), vpath.begin() + overlap, vpath.end());
		u = v;
	}
	return path;
}

/** 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);
}