void BedShuffle::ShuffleWithExclusions() {
int lineNum = 0;
BED bedEntry, nullBed; // used to store the current BED line from the BED file.
BedLineStatus bedStatus;
_bed->Open();
while ((bedStatus = _bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
if (bedStatus == BED_VALID) {
// keep looking as long as the chosen
// locus happens to overlap with regions
// that the user wishes to exclude.
int tries = 0;
bool haveOverlap = false;
do
{
// choose a new locus
ChooseLocus(bedEntry);
haveOverlap = _exclude->FindOneOrMoreOverlapsPerBin(bedEntry.chrom, bedEntry.start, bedEntry.end,
bedEntry.strand, false, _overlapFraction);
tries++;
} while ((haveOverlap == true) && (tries <= MAX_TRIES));
if (tries > MAX_TRIES) {
cerr << "Error, line " << lineNum << ": tried " << MAX_TRIES << " potential loci for entry, but could not avoid excluded regions. Ignoring entry and moving on." << endl;
}
else {
_bed->reportBedNewLine(bedEntry);
}
}
bedEntry = nullBed;
}
_bed->Close();
}
void BedShuffle::ShuffleWithExclusions() {
BED bedEntry;
_bed->Open();
while (_bed->GetNextBed(bedEntry)) {
if (_bed->_status == BED_VALID) {
// keep looking as long as the chosen
// locus happens to overlap with regions
// that the user wishes to exclude.
int tries = 0;
bool haveOverlap = false;
do
{
// choose a new locus
ChooseLocus(bedEntry);
haveOverlap = _exclude->anyHits(bedEntry.chrom, bedEntry.start, bedEntry.end,
bedEntry.strand, false, false, _overlapFraction, false);
tries++;
} while ((haveOverlap == true) && (tries <= MAX_TRIES));
if (tries > MAX_TRIES) {
cerr << "Error, line " << _bed->_lineNum << ": tried " << MAX_TRIES << " potential loci for entry, but could not avoid excluded regions. Ignoring entry and moving on." << endl;
}
else {
_bed->reportBedNewLine(bedEntry);
}
}
}
_bed->Close();
}
void BedShuffle::Shuffle() {
BED bedEntry;
_bed->Open();
while (_bed->GetNextBed(bedEntry)) {
if (_bed->_status == BED_VALID) {
ChooseLocus(bedEntry);
_bed->reportBedNewLine(bedEntry);
}
}
_bed->Close();
}
void BedShuffle::Shuffle() {
int lineNum = 0;
BED bedEntry, nullBed; // used to store the current BED line from the BED file.
BedLineStatus bedStatus;
_bed->Open();
while ((bedStatus = _bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
if (bedStatus == BED_VALID) {
ChooseLocus(bedEntry);
_bed->reportBedNewLine(bedEntry);
bedEntry = nullBed;
}
}
_bed->Close();
}
