Read CRAM input

[apeltzer]

As this uses the htsjdk already, it should support CRAM as input format. I'll add the required options, the reference option is already implemented here already ;-)

x-ref: nf-core/eager#181

[JudithNeukamm]

Hi Alex,
how urgent is this?
What do you mean with the 'reference option'?

[apeltzer]

Too long ago so I don#t know what I meant with this :-D

Urgent not so much, but we might add support for nf-core/eager to generate /output CRAM instead of BAM soonish, so then it would be beneficial to have direct support for CRAM in DamageProfiler to save conversion time 👍

As you use the htsjdk already as a library, it shouldn't require a lot actually to add this - probably 1-2 lines ...?

[JudithNeukamm]

True :) It Is implemented now and will be available with the next release.