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Fix for Issue #1023 #1026

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Fix for Issue #1023 #1026

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26 changes: 9 additions & 17 deletions src/pairToBed/pairToBed.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -97,14 +97,7 @@ void BedIntersectPE::FindOverlaps(const BEDPE &a, vector<BED> &hits1, vector<BED
// is there enough overlap relative to the user's request? (default ~ 1bp)
if ( ( (float) overlapBases / (float) aLength ) >= _overlapFraction ) {
numOverlapsEnd1++;

if (type == "either") {
_bedA->reportBedPETab(a);
_bedB->reportBedNewLine(*h);
}
else {
qualityHits1.push_back(*h);
}
qualityHits1.push_back(*h);
}
}
}
Expand All @@ -128,20 +121,18 @@ void BedIntersectPE::FindOverlaps(const BEDPE &a, vector<BED> &hits1, vector<BED
// is there enough overlap relative to the user's request? (default ~ 1bp)
if ( ( (float) overlapBases / (float) aLength ) >= _overlapFraction ) {
numOverlapsEnd2++;

if (type == "either") {
_bedA->reportBedPETab(a);
_bedB->reportBedNewLine(*h);
}
else {
qualityHits2.push_back(*h);
}
qualityHits2.push_back(*h);
}
}
}

// Now report the hits depending on what the user has requested.
if (type == "neither") {
if (type == "either") {
if ( (numOverlapsEnd1 > 0) || (numOverlapsEnd2 > 0) ) {
_bedA->reportBedPENewLine(a);
}
}
else if (type == "neither") {
if ( (numOverlapsEnd1 == 0) && (numOverlapsEnd2 == 0) ) {
_bedA->reportBedPENewLine(a);
}
Expand Down Expand Up @@ -189,6 +180,7 @@ void BedIntersectPE::FindOverlaps(const BEDPE &a, vector<BED> &hits1, vector<BED
}
}
}

}


Expand Down