void BedMap::Map() {
// create new BED file objects for A and B
_bedA = new BedFile(_bedAFile);
_bedB = new BedFile(_bedBFile);
// use the chromsweep algorithm to detect overlaps on the fly.
ChromSweep sweep = ChromSweep(_bedA, _bedB,
_sameStrand, _diffStrand,
_overlapFraction, _reciprocal,
_printHeader);
pair<BED, vector<BED> > hit_set;
hit_set.second.reserve(10000);
while (sweep.Next(hit_set)) {
string result = MapHits(hit_set.first, hit_set.second);
_bedA->reportBedTab(hit_set.first);
printf("%s\n", result.c_str());
}
}
unsigned long Jaccard::GetIntersection() {
_bedA = new BedFile(_bedAFile);
_bedB = new BedFile(_bedBFile);
unsigned long I = 0;
ChromSweep sweep = ChromSweep(_bedA, _bedB,
false, false,
_overlapFraction, _reciprocal,
true, false);
pair<BED, vector<BED> > hit_set;
hit_set.second.reserve(10000);
while (sweep.Next(hit_set)) {
I += GetTotalIntersection(hit_set.first, hit_set.second);
}
return I;
}
void BedIntersect::IntersectBed() {
// create new BED file objects for A and B
_bedA = new BedFile(_bedAFile);
_bedB = new BedFile(_bedBFile);
if (_sortedInput == false) {
// load the "B" file into a map in order to
// compare each entry in A to it in search of overlaps.
_bedB->loadBedFileIntoMap();
vector<BED> hits;
hits.reserve(100);
BED a;
// open the "A" file, process each BED entry and searh for overlaps.
_bedA->Open();
// report A's header first if asked.
if (_printHeader == true) {
_bedA->PrintHeader();
}
while (_bedA->GetNextBed(a)) {
if (_bedA->_status == BED_VALID) {
// treat the BED as a single "block"
if (_obeySplits == false)
FindOverlaps(a, hits);
// split the BED12 into blocks and look for overlaps in each discrete block
else {
// find the hits that overlap with the full span of the blocked BED
_bedB->allHits(a.chrom, a.start, a.end, a.strand,
hits, _sameStrand, _diffStrand,
_overlapFraction, _reciprocal);
// break a into discrete blocks, as we need to
// measure overlap with the individual blocks, not the full span.
bedVector a_blocks;
GetBedBlocks(a, a_blocks);
// find the overlaps between the block in A and B
// last parm is false as a is not a BAM entry
FindBlockedOverlaps(a, a_blocks, hits, false);
}
hits.clear();
}
}
_bedA->Close();
}
else {
// use the chromsweep algorithm to detect overlaps on the fly.
ChromSweep sweep = ChromSweep(_bedA, _bedB,
_sameStrand, _diffStrand,
_overlapFraction, _reciprocal,
_printHeader);
pair<BED, vector<BED> > hit_set;
hit_set.second.reserve(10000);
while (sweep.Next(hit_set)) {
if (_obeySplits == false)
processHits(hit_set.first, hit_set.second);
else {
bedVector a_blocks;
GetBedBlocks(hit_set.first, a_blocks);
FindBlockedOverlaps(hit_set.first, a_blocks, hit_set.second, false);
}
}
}
}
