Function outputNewContig

MergePaths/PathConsensus.cpp:298–347

Output a new contig. */

/** Output a new contig. */
static ContigNode outputNewContig(const Graph& g,
	const vector<Path>& solutions,
	size_t longestPrefix, size_t longestSuffix,
	const Sequence& seq, const unsigned coverage,
	ofstream& out)
{
	assert(!solutions.empty());
	assert(longestPrefix > 0);
	assert(longestSuffix > 0);

	size_t numContigs = num_vertices(g) / 2;
	ContigNode u(numContigs + g_newVertices.size(), false);
	string name = createContigName();
	put(vertex_name, g, u, name);
	out << '>' << name
		<< ' ' << seq.length() << ' ' << coverage << ' ';

	int dtu = INT_MAX, duv = INT_MAX;
	for (vector<Path>::const_iterator it = solutions.begin();
			it != solutions.end(); it++) {
		if (it != solutions.begin())
			out << ';';
		const ContigPath& path = *it;
		ContigPath::const_iterator
			first = path.begin() + longestPrefix,
			last = path.end() - longestSuffix;
		assert(first <= last);
		if (first < last) {
			ContigPath::const_iterator it = first;
			out << get(vertex_name, g, *it);
			for (++it; it != last; ++it)
				out << ',' << get(vertex_name, g, *it);
			dtu = min(dtu, getDistance(g, first[-1], first[0]));
			duv = min(duv, getDistance(g, last[-1], last[0]));
		} else
			out << '*';
	}
	out << '\n' << seq << '\n';
	assert(dtu < INT_MAX);
	assert(duv < INT_MAX);

	// Record the newly-created contig to be added to the graph later.
	g_newVertices.push_back(NewVertex(
				*(solutions[0].begin() + longestPrefix - 1),
				u,
				*(solutions[0].rbegin() + longestSuffix - 1),
				ContigProperties(seq.length(), coverage),
				dtu, duv));
	return u;
}

/** Return a consensus sequence of a and b.
 * @return an empty string if a consensus could not be found