Method processBranchesAssembly

Parallel/NetworkSequenceCollection.cpp:1288–1312

Processes branches that are in progress, removing those that have * completed. * @return the number of contigs and k-mer assembled */

 * @return the number of contigs and k-mer assembled
 */
pair<size_t, size_t> NetworkSequenceCollection::
processBranchesAssembly(FastaWriter* fileWriter, unsigned currContigID)
{
	size_t assembledContigs = 0, assembledKmer = 0;
	for (BranchGroupMap::iterator it = m_activeBranchGroups.begin();
			it != m_activeBranchGroups.end();) {
		if (!it->second.isActive()) {
			assert(it->second.size() == 1);
			BranchRecord& branch = it->second[0];
			assert(branch.getState() == BS_NOEXT
					|| branch.getState() == BS_AMBI_SAME
					|| branch.getState() == BS_AMBI_OPP);
			if ((opt::ss && branch.getDirection() == SENSE)
					|| (!opt::ss && branch.isCanonical())) {
				assembledContigs++;
				assembledKmer += branch.size();
				assembleContig(fileWriter, branch,
						m_numAssembled + currContigID++);
			}
			m_activeBranchGroups.erase(it++);
		} else
			++it;
	}
	return make_pair(assembledContigs, assembledKmer);
}

/** Send a request for the edges of vertex kmer. */
void NetworkSequenceCollection::generateExtensionRequest(