catch Sort BED case of non-unique BED ids

[owlang]

If a user provides a BED/CDT file of non-unique ids, Sort BED forces an output that can be misleading for the user.

1. Should we refactor ScriptManager to handle these BED/CDT files assuming a parallel sort or....
2. Should we add an error-checking handle and throw an exception for the user when non-unique IDs are encountered? (easier, faster implementation)

Whichever we choose, SortGFF should also be updated accordingly.