Check BED compatibility

[maxulysse]

Issue by @apeltzer, moved from SciLifeLab#687

Is your feature request related to a problem? Please describe.

Not really ;-) But this happens quite often when people use a target capture method.

Describe the solution you'd like

A small extra process that checks BED files for consistency with the utilized reference genome. Either check only and issue a warning or also offer to remove the chrprefix for example ;-)

Comments:

@apeltzer

Can do that if you guys don't mind :-)

@MaxUlysse

That would be amazing \o/