Function processGraph

RResolver/RAlgorithmsShort.cpp:922–1229

};

static void
processGraph(
    const Resolution& resolution,
    ImaginaryContigPaths& supportedPaths,
    ImaginaryContigPaths& unsupportedPaths)
{
	progressStart("New paths and vertices setup", resolution.repeatSupportMap.size() * 3);

	assert(!resolution.failed);

	std::vector<OldEdge> edges2remove;
	std::vector<NewEdge> edges2add;
	std::vector<NewVertex> vertices2add;

	std::map<int, std::vector<RepeatInstance>> repeatInstancesMap;

	size_t lastId = num_vertices(g_contigGraph) / 2;

	const auto start = resolution.repeatSupportMap.begin();
	const auto end = resolution.repeatSupportMap.end();

#ifdef _OPENMP
	int threads = omp_get_num_threads();
#else
	int threads = 1;
#endif

	// 1
	iteratorMultithreading(
	    start,
	    end,
	    [&](const std::pair<int, SupportMap>& repeatSupport) {
		    (void)repeatSupport;
		    return true;
	    },
	    [&](const std::pair<int, SupportMap>& repeatSupport) {
		    const auto repeat = ContigNode(repeatSupport.first);
		    const auto& supportMap = repeatSupport.second;

#pragma omp critical(repeatInstancesMap)
		    {
			    repeatInstancesMap.emplace(repeat.index(), std::vector<RepeatInstance>());
			    repeatInstancesMap.emplace((repeat ^ true).index(), std::vector<RepeatInstance>());
		    }

		    for (const auto& intigIdxAndOutigsSupp : supportMap) {
			    const auto intig = ContigNode(intigIdxAndOutigsSupp.first);
			    for (const auto& outigIdxAndSupp : intigIdxAndOutigsSupp.second) {
				    const auto outig = ContigNode(outigIdxAndSupp.first);
				    const auto& support = outigIdxAndSupp.second;
				    int dist1 = distanceBetween(intig, repeat);
				    int dist2 = distanceBetween(repeat, outig);

				    ImaginaryContigPath path = { { intig, 0 },
					                             { repeat, dist1 },
					                             { outig, dist2 } };

				    if (support.good()) {