check if BED follows standard format of 0 indexing

### Description of feature

in bin/subtract_variants.py 
  
It will be good to check if BED follows standard format of 0 indexing. Meaning if the bed indixeing does not start with 0 then this might be wrong here @heylf .
```
 if idx < len(chrom_regions):
        start, end = chrom_regions[idx]
        if pos >= start + 1 and pos <= end:
```