/************************************
Helper functions
************************************/
bool BedIntersect::processHits(const BED &a, const vector<BED> &hits) {
bool hitsFound = false;
if (_printable == true) {
// -wao the user wants to force the reporting of 0 overlap
if (hits.size() == 0) {
if (_writeAllOverlap) {
_bedA->reportBedTab(a);
_bedB->reportNullBedTab();
printf("0\n");
}
else if (_leftJoin) {
_bedA->reportBedTab(a);
_bedB->reportNullBedNewLine();
}
}
else {
vector<BED>::const_iterator h = hits.begin();
vector<BED>::const_iterator hitsEnd = hits.end();
for (; h != hitsEnd; ++h) {
CHRPOS s = max(a.start, h->start);
CHRPOS e = min(a.end, h->end);
int overlapBases = (e - s);
ReportOverlapDetail(overlapBases, a, *h, s, e);
hitsFound = true;
}
}
}
else {
ReportOverlapSummary(a, hits.size());
}
return hitsFound;
}
/************************************
Helper functions
************************************/
bool BedIntersect::processHits(const BED &a, const vector<BED> &hits, bool printable) {
// how many overlaps are there b/w the bed and the set of hits?
int s, e, overlapBases;
int numOverlaps = 0;
bool hitsFound = false;
int aLength = (a.end - a.start); // the length of a in b.p.
// loop through the hits and report those that meet the user's criteria
vector<BED>::const_iterator h = hits.begin();
vector<BED>::const_iterator hitsEnd = hits.end();
for (; h != hitsEnd; ++h) {
s = max(a.start, h->start);
e = min(a.end, h->end);
overlapBases = (e - s); // the number of overlapping bases b/w a and b
// is there enough overlap relative to the user's request? (default ~ 1bp)
if ( ( (float) overlapBases / (float) aLength ) >= _overlapFraction ) {
// Report the hit if the user doesn't care about reciprocal overlap between A and B.
if (_reciprocal == false) {
hitsFound = true;
numOverlaps++;
if (printable == true)
ReportOverlapDetail(overlapBases, a, *h, s, e);
}
// we require there to be sufficient __reciprocal__ overlap
else {
int bLength = (h->end - h->start);
float bOverlap = ( (float) overlapBases / (float) bLength );
if (bOverlap >= _overlapFraction) {
hitsFound = true;
numOverlaps++;
if (printable == true)
ReportOverlapDetail(overlapBases, a, *h, s, e);
}
}
}
}
// report the summary of the overlaps if requested.
ReportOverlapSummary(a, numOverlaps);
// were hits found for this BED feature?
return hitsFound;
}
