void BedShuffle::ShuffleWithInclusions() {
BED bedEntry; // used to store the current BED line from the BED file.
_bed->Open();
while (_bed->GetNextBed(bedEntry)) {
if (_bed->_status == BED_VALID) {
// choose a new locus
ChooseLocusFromInclusionFile(bedEntry);
_bed->reportBedNewLine(bedEntry);
}
}
_bed->Close();
}
void BedShuffle::ShuffleWithInclusions() {
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) {
// choose a new locus
ChooseLocusFromInclusionFile(bedEntry);
_bed->reportBedNewLine(bedEntry);
}
bedEntry = nullBed;
}
_bed->Close();
}
void BedShuffle::ChooseLocusFromInclusionFile(BED &bedEntry) {
string chrom = bedEntry.chrom;
CHRPOS length = bedEntry.end - bedEntry.start;
string randomChrom;
CHRPOS randomStart;
BED includeInterval;
if (_sameChrom == false) {
// grab a random chromosome from the inclusion file.
randomChrom = _includeChroms[rand() % _numIncludeChroms];
// get the number of inclusion intervals for that chrom
size_t size = _include->bedMapNoBin[randomChrom].size();
// grab a random interval on the chosen chromosome.
size_t interval = rand() % size;
// retreive a ranom -incl interval on the selected chrom
includeInterval = _include->bedMapNoBin[randomChrom][interval];
bedEntry.chrom = randomChrom;
}
else {
// get the number of inclusion intervals for the original chrom
size_t size = _include->bedMapNoBin[chrom].size();
// grab a random interval on the chosen chromosome.
includeInterval = _include->bedMapNoBin[chrom][rand() % size];
}
randomStart = includeInterval.start + rand() % (includeInterval.size());
bedEntry.start = randomStart;
bedEntry.end = randomStart + length;
// use recursion to ensure that the chosen location
// doesn't go past the end of the chrom
if (bedEntry.end > ((size_t) _genome->getChromSize(chrom))) {
//bedEntry.end = _genome->getChromSize(chrom);
ChooseLocusFromInclusionFile(bedEntry);
}
}