Method performNetworkDiscoverBubbles

Parallel/NetworkSequenceCollection.cpp:945–1007

Discover bubbles to pop. */

/** Discover bubbles to pop. */
size_t NetworkSequenceCollection::
performNetworkDiscoverBubbles()
{
	NetworkSequenceCollection* seqCollection = this;
	Timer timer("NetworkDiscoverBubbles");

	// The branch ids
	uint64_t branchGroupID = 0;
	m_finishedGroups.clear();

	// make sure the branch group structure is initially empty
	assert(m_activeBranchGroups.empty());

	size_t count = 0;

	// Set the cutoffs
	const unsigned maxNumBranches = 3;

	for (iterator iter = seqCollection->begin();
			iter != seqCollection->end(); ++iter) {
		if (iter->second.deleted())
			continue;

		if (++count % 100000 == 0)
			logger(1) << "Popping bubbles: " << count << '\n';

		SymbolSetPair extRec = iter->second.extension();
		for (extDirection dir = SENSE; dir <= ANTISENSE; ++dir) {
			if (extRec.dir[dir].isAmbiguous()) {
				BranchGroupMap::iterator groupIter
					= m_activeBranchGroups.insert(
						BranchGroupMap::value_type(branchGroupID,
							BranchGroup(dir, maxNumBranches,
								iter->first))).first;
				BranchGroup& group = groupIter->second;
				AssemblyAlgorithms::initiateBranchGroup(
						group, iter->first, extRec.dir[dir]);
				generateExtensionRequests(branchGroupID++,
						group.begin(), group.end());
			}
		}

		// Primitive load balancing
		if (m_activeBranchGroups.size() > MAX_ACTIVE) {
			while (m_activeBranchGroups.size() > LOW_ACTIVE) {
				seqCollection->pumpNetwork();
				processBranchesDiscoverBubbles();
			}
		}

		processBranchesDiscoverBubbles();
		seqCollection->pumpNetwork();
	}

	// Wait until the groups finish extending.
	while (processBranchesDiscoverBubbles())
		seqCollection->pumpNetwork();
	assert(m_activeBranchGroups.empty());