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 BedCoverage::CollectCoverageBed() {
// load the "B" bed file into a map so
// that we can easily compare "A" to it for overlaps
_bedB->loadBedCovFileIntoMap();
BED a;
_bedA->Open();
// process each entry in A
while (_bedA->GetNextBed(a)) {
if (_bedA->_status == BED_VALID) {
// process the BED entry as a single block
if (_obeySplits == false)
_bedB->countHits(a, _sameStrand, _diffStrand, _countsOnly);
// split the BED into discrete blocksand process each independently.
else {
bedVector bedBlocks;
GetBedBlocks(a, bedBlocks);
// use countSplitHits to avoid over-counting each split chunk
// as distinct read coverage.
_bedB->countSplitHits(bedBlocks, _sameStrand, _diffStrand, _countsOnly);
}
}
}
_bedA->Close();
// report the coverage (summary or histogram) for BED B.
if (_countsOnly == true)
ReportCounts();
else
ReportCoverage();
}
void BedCoverage::CollectCoverageBam(string bamFile) {
// load the "B" bed file into a map so
// that we can easily compare "A" to it for overlaps
_bedB->loadBedCovFileIntoMap();
// open the BAM file
BamReader reader;
reader.Open(bamFile);
// get header & reference information
string header = reader.GetHeaderText();
RefVector refs = reader.GetReferenceData();
// convert each aligned BAM entry to BED
// and compute coverage on B
BamAlignment bam;
while (reader.GetNextAlignment(bam)) {
if (bam.IsMapped()) {
// treat the BAM alignment as a single "block"
if (_obeySplits == false) {
// construct a new BED entry from the current BAM alignment.
BED a;
a.chrom = refs.at(bam.RefID).RefName;
a.start = bam.Position;
a.end = bam.GetEndPosition(false, false);
a.strand = "+";
if (bam.IsReverseStrand()) a.strand = "-";
_bedB->countHits(a, _sameStrand, _diffStrand, _countsOnly);
}
// split the BAM alignment into discrete blocks and
// look for overlaps only within each block.
else {
// vec to store the discrete BED "blocks" from a
bedVector bedBlocks;
// since we are counting coverage, we do want to split blocks when a
// deletion (D) CIGAR op is encountered (hence the true for the last parm)
GetBamBlocks(bam, refs.at(bam.RefID).RefName, bedBlocks, false, true);
// use countSplitHits to avoid over-counting each split chunk
// as distinct read coverage.
_bedB->countSplitHits(bedBlocks, _sameStrand, _diffStrand, _countsOnly);
}
}
}
// report the coverage (summary or histogram) for BED B.
if (_countsOnly == true)
ReportCounts();
else
ReportCoverage();
// close the BAM file
reader.Close();
}
