Function resolveShort

RResolver/RAlgorithmsShort.cpp:1259–1323

}

void
resolveShort(
    const std::vector<std::string>& readFilepaths,
    ImaginaryContigPaths& supportedPaths,
    ImaginaryContigPaths& unsupportedPaths)
{
	if (!determineShortReadStats(readFilepaths)) {
		return;
	}

	if (opt::verbose) {
		std::cerr << "\nRunning resolution algorithm...\n";
	}

	assert(g_contigSequences.size() > 0);
	assert(g_contigSequences.size() / 2 == g_contigComments.size());
	assert(ReadSize::readSizes.size() > 0);

	std::vector<std::pair<int, Histogram>> histograms;
	for (auto batch : ReadSize::readSizes) {
		ReadSize::current = batch;

		for (int r : ReadSize::current.rValues) {
			if (int(r) < int(opt::k)) {
				std::cerr << "r value " << r << "(" << ReadSize::current.size
				          << ") is too short - skipping." << std::endl;
				continue;
			}

			if (opt::verbose) {
				std::cerr << "\nRead size = " << batch.size << ", r = " << r << " ...\n\n";
			}

			buildFilters(readFilepaths, r, opt::bfMemFactor * double(opt::bloomSize));

			for (size_t j = 0; j < MAX_SUBITERATIONS; j++) {
				if (opt::verbose) {
					std::cerr << "\nSubiteration " << j + 1 << "...\n";
				}

				int unsupportedCountPrev = unsupportedPaths.size();

				Resolution resolution = resolveRepeats();

				if (!resolution.failed) {
					processGraph(resolution, supportedPaths, unsupportedPaths);
					assembleContigs();
					if (!opt::histPrefix.empty()) {
						writeHistograms(resolution, opt::histPrefix, j);
					}
				}

				int newUnsupportedCount = unsupportedPaths.size() - unsupportedCountPrev;
				assert(newUnsupportedCount >= 0);
				if (newUnsupportedCount == 0) {
					break;
				}
			}