Function trimSequences

Assembly/TrimAlgorithm.h:37–99

Prune tips shorter than maxBranchCull. */

/** Prune tips shorter than maxBranchCull. */
static inline
size_t trimSequences(SequenceCollectionHash* seqCollection,
		unsigned maxBranchCull)
{
	typedef SequenceCollectionHash Graph;
	typedef graph_traits<Graph>::vertex_descriptor V;
	typedef Graph::SymbolSetPair SymbolSetPair;

	Timer timer("TrimSequences");
	std::cout << "Pruning tips shorter than "
		<< maxBranchCull << " bp...\n";
	size_t numBranchesRemoved = 0;

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

		extDirection dir;
		// dir will be set to the trimming direction if the sequence
		// can be trimmed.
		SeqContiguity status = checkSeqContiguity(*iter, dir);

		if (status == SC_CONTIGUOUS)
			continue;
		else if(status == SC_ISLAND)
		{
			// remove this sequence, it has no extensions
			seqCollection->mark(iter->first);
			numBranchesRemoved++;
			continue;
		}

		BranchRecord currBranch(dir);
		V currSeq = iter->first;
		while(currBranch.isActive())
		{
			SymbolSetPair extRec;
			int multiplicity = -1;
			bool success = seqCollection->getSeqData(
					currSeq, extRec, multiplicity);
			assert(success);
			(void)success;
			processLinearExtensionForBranch(currBranch,
					currSeq, extRec, multiplicity, maxBranchCull);
		}

		// The branch has ended check it for removal, returns true if
		// it was removed.
		if(processTerminatedBranchTrim(seqCollection, currBranch))
		{
			numBranchesRemoved++;
		}
		seqCollection->pumpNetwork();
	}

	size_t numSweeped = removeMarked(seqCollection);