Method controlCoverage

Parallel/NetworkSequenceCollection.cpp:393–454

Remove low-coverage contigs. */

/** Remove low-coverage contigs. */
void NetworkSequenceCollection::controlCoverage()
{
	assert(opt::coverage > 0);

	// Split ambiguous branches.
	SetState(NAS_MARK_AMBIGUOUS);
	controlMarkAmbiguous();

	// Remove low-coverage contigs.
	cout << "Removing low-coverage contigs "
			"(mean k-mer coverage < " << opt::coverage << ")...\n";
	SetState(NAS_COVERAGE);
	m_comm.sendControlMessage(APC_SET_STATE, NAS_COVERAGE);
	m_comm.reduce(m_data.cleanup());
	m_lowCoverageContigs = 0;
	m_lowCoverageKmer = 0;
	pair<size_t, size_t> numAssembled
		= performNetworkAssembly();
	EndState();

	m_numReachedCheckpoint++;
	while (!checkpointReached())
		pumpNetwork();

	// Count the number of low-coverage contigs.
	SetState(NAS_COVERAGE_COMPLETE);
	m_comm.sendControlMessage(APC_SET_STATE, NAS_COVERAGE_COMPLETE);
	m_comm.barrier();
	pumpNetwork();

	numAssembled.first = m_comm.reduce(numAssembled.first);
	numAssembled.second = m_comm.reduce(numAssembled.second);
	cout << "Found " << numAssembled.second << " k-mer in "
		<< numAssembled.first << " contigs "
			"before removing low-coverage contigs.\n";

	size_t lowCoverageContigs = m_comm.reduce(m_lowCoverageContigs);
	size_t lowCoverageKmer = m_comm.reduce(m_lowCoverageKmer);
	cout << "Removed " << lowCoverageKmer << " k-mer in "
		<< lowCoverageContigs << " low-coverage contigs.\n";

	if (!opt::db.empty()) {
		AssemblyAlgorithms::addToDb ("totalLowCovCntg", lowCoverageContigs);
		AssemblyAlgorithms::addToDb ("totalLowCovKmer", lowCoverageKmer);
	}

	EndState();

	SetState(NAS_SPLIT_AMBIGUOUS);
	controlSplitAmbiguous();

	SetState(NAS_CLEAR_FLAGS);
	m_comm.sendControlMessage(APC_SET_STATE, NAS_CLEAR_FLAGS);
	m_comm.barrier();
	pumpNetwork();
	m_data.wipeFlag(SeqFlag(SF_MARK_SENSE | SF_MARK_ANTISENSE));
	size_t removed = m_comm.reduce(m_data.cleanup());
	cout << "Removed " << removed << " marked k-mer.\n";