Function mergePath

MergePaths/MergePaths.cpp:392–430

Merge the paths of the specified seed path. * @return the merged contig 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;
}

/** A collection of contig paths. */
typedef vector<ContigPath> ContigPaths;