Cram references STILL not working
Created by: agraubert
I was pretty sure we fixed the issue with cram references back in walaj/SeqLib#38, but apparently travis builds are still failing. Somehow, despite a reference being handed to SeqLib and SeqLib setting the reference on the HTSlib bam object we still can't read Crams unless the fasta is in the hts cache or at the location indicated in the bam header.
I unfortunately don't have time to work on this right now, so for the time being I'm adding a warning message to RNA-SeQC and disabling tests on crams