Manage bed specification for both bed and region

[tdelhomme]

We need to manage the bed file specification for both bed input and region input.
This is describe here:

chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.

This needs to be adapted to --region input to samtools, where end position is taking into account.