Method GetNextMergedBed

src/utils/bedFile/bedFile.cpp:274–326

bool BedFile::GetNextMergedBed(BED &merged_bed) {

    if (_bedStream->good()) {
        BED bed;
        // force sorting; hence third param = true
        while (GetNextBed(bed, true)) {
            if (_status == BED_VALID) {
                if ((bed.start - _merged_end > 0) || 
                   (_merged_end < 0) || 
                   (bed.chrom != _merged_chrom))
                {
                    if (_merged_start >= 0) {
                        merged_bed.chrom = _merged_chrom;
                        merged_bed.start = _merged_start;
                        merged_bed.end   = _merged_end;

                        _merged_chrom = bed.chrom;
                        _merged_start = bed.start;
                        _merged_end   = bed.end;

                        _total_flattened_length += \
                            (merged_bed.end - merged_bed.start);
                        return true;
                    }
                    else {
                        _merged_start = bed.start;
                        _merged_chrom = bed.chrom;
                        _merged_end = bed.end;
                    }
                }
                else if (bed.end > _merged_end)
                {   
                    _merged_end = bed.end;
                }
            }
        }

        // handle the last merged block in the file.
        if (_status == BED_INVALID)
        {
            _status = BED_VALID;
            merged_bed.chrom = _merged_chrom;
            merged_bed.start = _merged_start;
            merged_bed.end   = _merged_end;
            
            _total_flattened_length += \
                (merged_bed.end - merged_bed.start);
            return true;
        }
    }
    _status = BED_INVALID;
    return false;
}


unsigned long BedFile::getTotalLength(void) {