Method controlErode

Parallel/NetworkSequenceCollection.cpp:286–325

}

size_t NetworkSequenceCollection::controlErode()
{
	SetState(NAS_ERODE);
	m_comm.sendControlMessage(APC_SET_STATE, NAS_ERODE);
	m_comm.barrier();
	size_t numEroded = AssemblyAlgorithms::erodeEnds(this);
	EndState();

	// Do not call SetState, because it clears the
	// checkpoint information.
	//SetState(NAS_ERODE_WAITING);
	m_state = NAS_ERODE_WAITING;

	m_numReachedCheckpoint++;
	while (!checkpointReached())
		pumpNetwork();
	numEroded += m_checkpointSum;
	EndState();

	if (numEroded == 0) {
		SetState(NAS_WAITING);
		m_comm.sendControlMessage(APC_WAIT);
		m_comm.barrier();
		return 0;
	}

	SetState(NAS_ERODE_COMPLETE);
	m_comm.sendControlMessage(APC_ERODE_COMPLETE);
	completeOperation();
	numEroded += m_comm.reduce(
			AssemblyAlgorithms::getNumEroded());
	cout << "Eroded " << numEroded << " tips.\n";
	size_t removed = m_comm.reduce(m_data.cleanup());
	m_comm.barrier();
	assert(removed == numEroded);
	(void)removed;

	SetState(NAS_WAITING);
	return numEroded;
}

/** Remove marked k-mer.
 * @return the number of k-mer removed