Support for both CRAM and BAM at the same time

[LouisLeNezet]

Description of feature

The input file need for the moment all the files to be of the same type.
Is it something we want to keep or do should the user be able to give a mixture of format ?
I proprose to keep to one type for the moment and if user ask for this feature to add it in the next versions.

[atrigila]

I agree and I think it would be better that the input format is always the same.