Function resolveRepeats

RResolver/RAlgorithmsShort.cpp:689–834

}

static Resolution
resolveRepeats()
{
	long total = (num_vertices(g_contigGraph) - num_vertices_removed(g_contigGraph)) / 2;
	long repeats = 0;
	long pathsSupported = 0, pathsUnsupported = 0;
	std::vector<Support> supports;

	progressStart(
	    "Path resolution (r = " + std::to_string(g_vanillaBloom->get_k()) + ")", total * 2);

	Resolution resolution(ReadSize::current, g_vanillaBloom->get_k());

	Graph::vertex_iterator vertexStart, vertexEnd;
	boost::tie(vertexStart, vertexEnd) = vertices(g_contigGraph);

	iteratorMultithreading(
	    vertexStart,
	    vertexEnd,
	    [&](const ContigNode& node) {
		    if (!get(vertex_removed, g_contigGraph, node)) {
			    if (isSmallRepeat(node)) {
				    return true;
			    } else {
#pragma omp critical(cerr)
				    progressUpdate();
				    return false;
			    }
		    }
		    return false;
	    },
	    [&](const ContigNode& node) {
		    bool inHistSample;
		    bool skip = false;
#pragma omp critical(resolution)
		    {
			    repeats++;
			    inHistSample = (repeats <= HIST_SAMPLE_SIZE);
			    skip = (repeats > REPEAT_CASES_LIMIT);
		    }

		    if (!skip) {
			    auto supportMap = buildRepeatSupportMap(node);

#pragma omp critical(resolution)
			    {
				    resolution.repeatSupportMap[node.index()] = supportMap;
				    updateStats(resolution, supports, supportMap, inHistSample);
			    }
		    }

#pragma omp critical(cerr)
		    progressUpdate();
	    });

	long pathsKnown = 0, pathsUnknown = 0, pathsTotal = 0;
	static const std::string unknownReasonLabels[] = { "Undetermined", "Too many combinations", "Over max tests", "Possible tests < planned tests", "Window not long enough", "Head shorter than margin", "Tail shorter than margin", "Different culprit" };
	static const size_t unknownReasons = countof(unknownReasonLabels);