Function fragmentSize

ParseAligns/ParseAligns.cpp:130–138

* Return the size of the fragment demarcated by the specified * alignments. */

 * alignments.
 */
static int
fragmentSize(const Alignment& a0, const Alignment& a1)
{
	assert(a0.contig == a1.contig);
	assert(a0.isRC != a1.isRC);
	const Alignment& f = a0.isRC ? a1 : a0;
	const Alignment& r = a0.isRC ? a0 : a1;
	return r - f;
}

typedef pair<ContigNode, DistanceEst> Estimate;
typedef vector<Estimate> Estimates;