Read CRAM input
apeltzer opened this issue · 3 comments
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
Hi Alex,
how urgent is this?
What do you mean with the 'reference option'?
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 ...?
True :) It Is implemented now and will be available with the next release.