Function writeBubble

Assembly/BubbleAlgorithm.h:224–241

Write a bubble to the specified file. */

/** Write a bubble to the specified file. */
static inline
void writeBubble(std::ostream& out, const BranchGroup& group, unsigned id)
{
	if (opt::snpPath.empty())
		return;

	char allele = 'A';
	for (BranchGroup::const_iterator it = group.begin();
			it != group.end(); ++it) {
		const BranchRecord& currBranch = *it;
		Sequence contig(currBranch);
		out << '>' << id << allele++ << ' '
			<< contig.length() << ' '
			<< currBranch.calculateBranchMultiplicity() << '\n'
			<< contig.c_str() << '\n';
	}
	assert_good(out, opt::snpPath);
}

/** Collapse a bubble to a single path. */
template <typename Graph>