Function assembleContig

Assembly/AssembleAlgorithm.h:14–39

 */
template <typename Graph>
size_t assembleContig(
		Graph* seqCollection, FastaWriter* writer,
		BranchRecord& branch, unsigned id)
{
	assert(!branch.isActive());
	assert(branch.getState() == BS_NOEXT
			|| branch.getState() == BS_AMBI_SAME
			|| branch.getState() == BS_AMBI_OPP);

	// Assemble the contig.
	Sequence contig(branch);

	size_t kmerCount = branch.calculateBranchMultiplicity();
	if (writer != NULL)
		writer->WriteSequence(contig, id, kmerCount);

	// Remove low-coverage contigs.
	float coverage = (float)kmerCount / branch.size();
	if (opt::coverage > 0 && coverage < opt::coverage) {
		for (BranchRecord::iterator it = branch.begin();
				it != branch.end(); ++it)
			seqCollection->remove(it->first);
		return branch.size();
	}
	return 0;
}

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