Function flipAlignment

ParseAligns/ParseAligns.cpp:302–306

* Return an alignment flipped as necessary to produce an alignment * pair whose expected orientation is forward-reverse. If the * expected orientation is forward-forward, then reverse the first * alignment, so that the alignment is forward-reverse, which is * required by DistanceEst. */

 * required by DistanceEst.
 */
static const Alignment
flipAlignment(const Alignment& a, const string& id)
{
	return needsFlipping(id) ? a.flipQuery() : a;
}

static void
handleAlignmentPair(const ReadAlignMap::value_type& curr, const ReadAlignMap::value_type& pair)