Full per base output despite 'by' region definition
When specifying regions to output from a bed file (in 0.1.19 release binary), the per-base output is for the entire genome. While this might be the desired behavior, I'd rather get the per-base limited to the same as that specified via by/bed. 

In that regard, I'd recommend two separate options:

1. `--by`: specifying interval lengths.
2. `--region` (or `--bed` or something): specifying specifying a file with regions (bed-file).

Currently, the two available `--by` behaviors are quite different. In the second case, IMHO the per-base output in the 2nd case should be limited to the requested region(s).