Function expectedSpacingBetweenReads

RResolver/RAlgorithmsShort.cpp:419–446

}

static double
expectedSpacingBetweenReads(const ContigPath& path)
{
	assert(path.size() >= 3);
	const long pathLength = 1000000; // Use long path lenth in order to calculate numbers asymptotically
	std::vector<double> contigBaseCoverages;
	for (const auto& node : path) {
		contigBaseCoverages.push_back(getContigBaseCoverage(node));
	}
	const double pathBaseCoverage = *std::min_element(contigBaseCoverages.begin(), contigBaseCoverages.end());
	const double pathBases = pathBaseCoverage * pathLength;

	double meanReadKmerContribution = 0;
	for (const auto& batch : ReadSize::readSizes) {
		meanReadKmerContribution += batch.getFractionOfTotal() * (batch.size - opt::k + 1);
	}
	const double baseContributionRatio = ReadSize::current.getFractionOfTotal() *
	                                     (ReadSize::current.size - opt::k + 1) /
	                                     meanReadKmerContribution;

	const double approxNumOfReads = double(pathBases * baseContributionRatio) /
	                                double(opt::k * (ReadSize::current.size - opt::k + 1));
	assert(approxNumOfReads > 2);

	const double expectedSpacing = std::max(double(1.0), double(pathLength - ReadSize::current.size + 1) / double(approxNumOfReads));

	return expectedSpacing;
}

static Support
determinePathSupport(const ContigPath& path)