// Coalesce a set of alignments into distinct locations
void HapgenUtil::coalesceAlignments(HapgenAlignmentVector& alignments)
{
if(alignments.empty())
return;
// Sort the alignments by reference id, then position
std::sort(alignments.begin(), alignments.end());
HapgenAlignmentVector outAlignments;
// Iterate over the alignments in sorted order
// If an alignment is distinct (=does not overlap) from the
// previous alignment, add it to the output collection.
// First alignment is always ok
outAlignments.push_back(alignments[alignments.size()-1]);
// Kees: start from back because alignments are sorted in order of increasing score
for(size_t i = alignments.size()-1; i-- > 0;)
{
// Check this alignment against the last alignment added to the output set
HapgenAlignment& prevAlign = outAlignments.back();
const HapgenAlignment& currAlign = alignments[i];
int s1 = prevAlign.position;
int e1 = s1 + prevAlign.length;
int s2 = currAlign.position;
int e2 = s2 + currAlign.length;
bool intersecting = Interval::isIntersecting(s1, e1, s2, e2);
if(prevAlign.referenceID != currAlign.referenceID || !intersecting)
{
outAlignments.push_back(currAlign);
}
else
{
// merge the intersecting alignment into a window that covers both
prevAlign.position = std::min(s1, s2);
prevAlign.length = std::max(e1, e2) - prevAlign.position;
}
}
alignments = outAlignments;
}
