void BedCoverage::CollectCoverageBed() {
// load the "B" bed file into a map so
// that we can easily compare "A" to it for overlaps
_bedB->loadBedCovFileIntoMap();
int lineNum = 0; // current input line number
BED a, nullBed;
BedLineStatus bedStatus;
_bedA->Open();
// process each entry in A
while ((bedStatus = _bedA->GetNextBed(a, lineNum)) != BED_INVALID) {
if (bedStatus == BED_VALID) {
// process the BED entry as a single block
if (_obeySplits == false)
_bedB->countHits(a, _forceStrand);
// split the BED into discrete blocksand process each independently.
else {
bedVector bedBlocks;
splitBedIntoBlocks(a, lineNum, bedBlocks);
// use countSplitHits to avoid over-counting each split chunk
// as distinct read coverage.
_bedB->countSplitHits(bedBlocks, _forceStrand);
}
a = nullBed;
}
}
_bedA->Close();
// report the coverage (summary or histogram) for BED B.
ReportCoverage();
}
void BedIntersect::IntersectBed() {
// load the "B" file into a map in order to
// compare each entry in A to it in search of overlaps.
_bedB->loadBedFileIntoMap();
int lineNum = 0;
vector<BED> hits;
hits.reserve(100);
BED a, nullBed;
BedLineStatus bedStatus;
// open the "A" file, process each BED entry and searh for overlaps.
_bedA->Open();
while ((bedStatus = _bedA->GetNextBed(a, lineNum)) != BED_INVALID) {
if (bedStatus == BED_VALID) {
// treat the BED as a single "block"
if (_obeySplits == false) {
FindOverlaps(a, hits);
hits.clear();
a = nullBed;
}
// split the BED12 into blocks and look for overlaps in each discrete block
else {
bedVector bedBlocks; // vec to store the discrete BED "blocks"
splitBedIntoBlocks(a, lineNum, bedBlocks);
vector<BED>::const_iterator bedItr = bedBlocks.begin();
vector<BED>::const_iterator bedEnd = bedBlocks.end();
for (; bedItr != bedEnd; ++bedItr) {
FindOverlaps(*bedItr, hits);
hits.clear();
}
a = nullBed;
}
}
}
_bedA->Close();
}
