void PairToPair::FindOverlaps(const BEDPE &a) {
//
vector<MATE> hitsA1B1, hitsA1B2, hitsA2B1, hitsA2B2;
// add the appropriate slop to the starts and ends
int start1 = a.start1;
int end1 = a.end1;
int start2 = a.start2;
int end2 = a.end2;
if (_strandedSlop == true) {
if (a.strand1 == "+")
end1 += _slop;
else
start1 -= _slop;
if (a.strand2 == "+")
end2 += _slop;
else
start2 -= _slop;
}
else {
(start1 - _slop) >= 0 ? start1 -= _slop : start1 = 0;
(start2 - _slop) >= 0 ? start2 -= _slop : start2 = 0;
end1 += _slop;
end2 += _slop;
}
// Find the _potential_ hits between each end of A and B
_bedB->FindOverlapsPerBin(1, a.chrom1, start1, end1, a.name, a.strand1, hitsA1B1, _overlapFraction, !(_ignoreStrand), _reqDiffNames); // hits b/w A1 & B1
_bedB->FindOverlapsPerBin(1, a.chrom2, start2, end2, a.name, a.strand2, hitsA2B1, _overlapFraction, !(_ignoreStrand), _reqDiffNames); // hits b/w A2 & B1
_bedB->FindOverlapsPerBin(2, a.chrom1, start1, end1, a.name, a.strand1, hitsA1B2, _overlapFraction, !(_ignoreStrand), _reqDiffNames); // hits b/w A1 & B2
_bedB->FindOverlapsPerBin(2, a.chrom2, start2, end2, a.name, a.strand2, hitsA2B2, _overlapFraction, !(_ignoreStrand), _reqDiffNames); // hits b/w A2 & B2
unsigned int matchCount1 = (hitsA1B1.size() + hitsA2B2.size());
unsigned int matchCount2 = (hitsA2B1.size() + hitsA1B2.size());
// report the fact that no hits were found iff _searchType is neither.
if ((matchCount1 == 0) && (matchCount2 == 0) && (_searchType == "neither")) {
_bedA->reportBedPENewLine(a);
}
else if (_searchType == "both") {
bool found1 = false;
bool found2 = false;
if ((hitsA1B1.size() > 0) || (hitsA2B2.size() > 0))
found1 = FindHitsOnBothEnds(a, hitsA1B1, hitsA2B2);
if ((hitsA2B1.size() > 0) || (hitsA1B2.size() > 0))
found2 = FindHitsOnBothEnds(a, hitsA2B1, hitsA1B2);
}
else if (_searchType == "notboth") {
bool found1 = false;
bool found2 = false;
if ((hitsA1B1.size() > 0) || (hitsA2B2.size() > 0))
found1 = FindHitsOnBothEnds(a, hitsA1B1, hitsA2B2);
if ((hitsA2B1.size() > 0) || (hitsA1B2.size() > 0))
found2 = FindHitsOnBothEnds(a, hitsA2B1, hitsA1B2);
if (found1 == false && found2 == false)
_bedA->reportBedPENewLine(a);
}
else if (_searchType == "either") {
FindHitsOnEitherEnd(a, hitsA1B1, hitsA2B2);
FindHitsOnEitherEnd(a, hitsA2B1, hitsA1B2);
}
}
void PairToPair::FindOverlaps(const BEDPE &a, vector<BEDCOV> &hitsA1B1, vector<BEDCOV> &hitsA1B2,
vector<BEDCOV> &hitsA2B1, vector<BEDCOV> &hitsA2B2) {
// list of hits on each end of BEDPE
// that exceed the requested overlap fraction
vector<BEDCOV> qualityHitsA1B1;
vector<BEDCOV> qualityHitsA1B2;
vector<BEDCOV> qualityHitsA2B1;
vector<BEDCOV> qualityHitsA2B2;
// count of hits on each end of BEDPE
// that exceed the requested overlap fraction
int numOverlapsA1B1 = 0;
int numOverlapsA1B2 = 0;
int numOverlapsA2B1 = 0;
int numOverlapsA2B2 = 0;
// add the appropriate slop to the starts and ends
CHRPOS start1 = a.start1;
CHRPOS end1 = a.end1;
CHRPOS start2 = a.start2;
CHRPOS end2 = a.end2;
if (_strandedSlop == true) {
if (a.strand1 == "+")
end1 += _slop;
else
start1 -= _slop;
if (a.strand2 == "+")
end2 += _slop;
else
start2 -= _slop;
}
else {
start1 -= _slop;
start2 -= _slop;
end1 += _slop;
end2 += _slop;
}
// Find the _potential_ hits between each end of A and B
_bedB->FindOverlapsPerBin(1, a.chrom1, start1, end1, a.strand1, hitsA1B1, !(_ignoreStrand)); // hits b/w A1 & B1
_bedB->FindOverlapsPerBin(1, a.chrom2, start2, end2, a.strand2, hitsA2B1, !(_ignoreStrand)); // hits b/w A2 & B1
_bedB->FindOverlapsPerBin(2, a.chrom1, start1, end1, a.strand1, hitsA1B2, !(_ignoreStrand)); // hits b/w A1 & B2
_bedB->FindOverlapsPerBin(2, a.chrom2, start2, end2, a.strand2, hitsA2B2, !(_ignoreStrand)); // hits b/w A2 & B2
// Now, reduce to the set of hits on each end of A and B
// that meet the required overlap fraction and orientation.
// FindQualityHitsBetweenEnds(start1, end1, start2, end2, hitsA1B1, qualityHitsA1B1, numOverlapsA1B1); // quality hits b/w A1 & B1
// FindQualityHitsBetweenEnds(start1, end1, start2, end2, hitsA1B2, qualityHitsA1B2, numOverlapsA1B2); // quality hits b/w A1 & B2
// FindQualityHitsBetweenEnds(start1, end1, start2, end2, hitsA2B1, qualityHitsA2B1, numOverlapsA2B1); // quality hits b/w A2 & B1
// FindQualityHitsBetweenEnds(start1, end1, start2, end2, hitsA2B2, qualityHitsA2B2, numOverlapsA2B2); // quality hits b/w A2 & B2
FindQualityHitsBetweenEnds(start1, end1, hitsA1B1, qualityHitsA1B1, numOverlapsA1B1); // quality hits b/w A1 & B1
FindQualityHitsBetweenEnds(start1, end1, hitsA1B2, qualityHitsA1B2, numOverlapsA1B2); // quality hits b/w A1 & B2
FindQualityHitsBetweenEnds(start2, end2, hitsA2B1, qualityHitsA2B1, numOverlapsA2B1); // quality hits b/w A2 & B1
FindQualityHitsBetweenEnds(start2, end2, hitsA2B2, qualityHitsA2B2, numOverlapsA2B2); // quality hits b/w A2 & B2
int matchCount1 = 0;
int matchCount2 = 0;
if (_searchType == "neither" || _searchType == "both") {
if ((numOverlapsA1B1 > 0) || (numOverlapsA2B2 > 0))
FindHitsOnBothEnds(a, qualityHitsA1B1, qualityHitsA2B2, matchCount1);
if ((numOverlapsA1B2 > 0) || (numOverlapsA2B1 > 0))
FindHitsOnBothEnds(a, qualityHitsA2B1, qualityHitsA1B2, matchCount2);
// report the fact that no hits were found iff _searchType is neither.
if ((matchCount1 == 0) && (matchCount2 == 0) && (_searchType == "neither")) {
_bedA->reportBedPENewLine(a);
}
}
else if (_searchType == "either") {
FindHitsOnEitherEnd(a, qualityHitsA1B1, qualityHitsA2B2, matchCount1);
FindHitsOnEitherEnd(a, qualityHitsA2B1, qualityHitsA1B2, matchCount2);
}
}