void BedClosest::FindClosestBed() {
// load the "B" bed file into a map so
// that we can easily compare "A" to it for overlaps
_bedB->loadBedFileIntoMap();
BED a, nullBed;
int lineNum = 0; // current input line number
vector<BED> hits; // vector of potential hits
hits.reserve(100);
BedLineStatus bedStatus;
_bedA->Open();
// process each entry in A in search of the closest feature in B
while ((bedStatus = _bedA->GetNextBed(a, lineNum)) != BED_INVALID) {
if (bedStatus == BED_VALID) {
FindWindowOverlaps(a, hits);
hits.clear();
a = nullBed;
}
}
_bedA->Close();
}
void BedWindow::WindowIntersectBed() {
// load the "B" bed file into a map so
// that we can easily compare "A" to it for overlaps
_bedB->loadBedFileIntoMap();
BED a;
vector<BED> hits;
hits.reserve(100);
_bedA->Open();
// report A's header first if asked.
if (_printHeader == true) {
_bedA->PrintHeader();
}
while (_bedA->GetNextBed(a)) {
if (_bedA->_status == BED_VALID) {
FindWindowOverlaps(a, hits);
hits.clear();
}
}
_bedA->Close();
}
void BedWindow::WindowIntersectBam(string bamFile) {
// load the "B" bed file into a map so
// that we can easily compare "A" to it for overlaps
_bedB->loadBedFileIntoMap();
// open the BAM file
BamReader reader;
BamWriter writer;
reader.Open(bamFile);
// get header & reference information
string bamHeader = reader.GetHeaderText();
RefVector refs = reader.GetReferenceData();
// open a BAM output to stdout if we are writing BAM
if (_bamOutput == true) {
// set compression mode
BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
if ( _isUncompressedBam ) compressionMode = BamWriter::Uncompressed;
writer.SetCompressionMode(compressionMode);
// open our BAM writer
writer.Open("stdout", bamHeader, refs);
}
vector<BED> hits; // vector of potential hits
// reserve some space
hits.reserve(100);
_bedA->bedType = 6;
BamAlignment bam;
bool overlapsFound;
// get each set of alignments for each pair.
while (reader.GetNextAlignment(bam)) {
if (bam.IsMapped()) {
BED a;
a.chrom = refs.at(bam.RefID).RefName;
a.start = bam.Position;
a.end = bam.GetEndPosition(false, false);
// build the name field from the BAM alignment.
a.name = bam.Name;
if (bam.IsFirstMate()) a.name += "/1";
if (bam.IsSecondMate()) a.name += "/2";
a.score = ToString(bam.MapQuality);
a.strand = "+"; if (bam.IsReverseStrand()) a.strand = "-";
if (_bamOutput == true) {
overlapsFound = FindOneOrMoreWindowOverlaps(a);
if (overlapsFound == true) {
if (_noHit == false)
writer.SaveAlignment(bam);
}
else {
if (_noHit == true)
writer.SaveAlignment(bam);
}
}
else {
FindWindowOverlaps(a, hits);
hits.clear();
}
}
// BAM IsMapped() is false
else if (_noHit == true) {
writer.SaveAlignment(bam);
}
}
// close the relevant BAM files.
reader.Close();
if (_bamOutput == true) {
writer.Close();
}
}