Method performNetworkAssembly

Parallel/NetworkSequenceCollection.cpp:1199–1282

Assemble contigs. * @return the number of contigs and k-mer assembled */

 * @return the number of contigs and k-mer assembled
 */
pair<size_t, size_t> NetworkSequenceCollection::
performNetworkAssembly(FastaWriter* fileWriter)
{
	Timer timer("NetworkAssembly");
	NetworkSequenceCollection* seqCollection = this;
	pair<size_t, size_t> numAssembled(0, 0);
	uint64_t branchGroupID = 0;
	assert(m_activeBranchGroups.empty());

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

		extDirection dir;
		// dir will be set to the assembly direction if the sequence
		// can be assembled.
		SeqContiguity status = AssemblyAlgorithms::checkSeqContiguity(
				*iter, dir, true);
		if (status == SC_CONTIGUOUS)
			continue;
		else if(status == SC_ISLAND)
		{
			// Output the singleton contig.
			BranchRecord currBranch(SENSE);
			currBranch.push_back(*iter);
			currBranch.terminate(BS_NOEXT);
			assembleContig(fileWriter, currBranch,
					m_numAssembled + numAssembled.first);
			numAssembled.first++;
			numAssembled.second += currBranch.size();
			continue;
		}

		BranchGroup group(dir, 1, iter->first);
		group.addBranch(BranchRecord(dir));
		pair<BranchGroupMap::iterator, bool>
			inserted = m_activeBranchGroups.insert(
				BranchGroupMap::value_type(branchGroupID, group));
		assert(inserted.second);

		// Generate the first extension request
		BranchRecord& branch = inserted.first->second[0];
		branch.push_back(*iter);
		V kmer = iter->first;
		AssemblyAlgorithms::extendBranch(branch,
				kmer, iter->second.getExtension(dir));
		assert(branch.isActive());
		generateExtensionRequest(branchGroupID++, 0, kmer);

		numAssembled += processBranchesAssembly(
				fileWriter, numAssembled.first);
		seqCollection->pumpNetwork();

		if(m_activeBranchGroups.size() > MAX_ACTIVE)
		{
			while(m_activeBranchGroups.size() > LOW_ACTIVE)
			{