Function assemble

Assembly/AssembleAlgorithm.h:44–142

Assemble contigs. * @return the number of contigs assembled */

 * @return the number of contigs assembled
 */
static inline
size_t assemble(SequenceCollectionHash* seqCollection,
		FastaWriter* fileWriter = NULL)
{
	typedef SequenceCollectionHash Graph;
	typedef graph_traits<Graph>::vertex_descriptor V;
	typedef Graph::SymbolSetPair SymbolSetPair;

	Timer timer("Assemble");

	size_t kmerCount = 0;
	unsigned contigID = 0;
	size_t assembledKmer = 0;
	size_t lowCoverageKmer = 0;
	size_t lowCoverageContigs = 0;

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

		extDirection dir;
		SeqContiguity status = checkSeqContiguity(*iter, dir, true);
		if (status == SC_CONTIGUOUS)
			continue;
		else if(status == SC_ISLAND)
		{
			BranchRecord currBranch(SENSE);
			currBranch.push_back(*iter);
			currBranch.terminate(BS_NOEXT);
			size_t removed = assembleContig(seqCollection,
					fileWriter, currBranch, contigID++);
			assembledKmer += currBranch.size();
			if (removed > 0) {
				lowCoverageContigs++;
				lowCoverageKmer += removed;
			}
			continue;
		}
		assert(status == SC_ENDPOINT);

		BranchRecord currBranch(dir);
		currBranch.push_back(*iter);
		V currSeq = iter->first;
		extendBranch(currBranch, currSeq,
				iter->second.getExtension(dir));
		assert(currBranch.isActive());
		while(currBranch.isActive())
		{
			SymbolSetPair extRec;
			int multiplicity = -1;
			bool success = seqCollection->getSeqData(
					currSeq, extRec, multiplicity);
			assert(success);
			(void)success;
			processLinearExtensionForBranch(currBranch,
					currSeq, extRec, multiplicity, UINT_MAX);