Collapse the fasta reference

[jayhesselberth]

I am not convinced that having multiple isodecoders in the alignment reference is helpful, and it makes calculating differential expression the right way (using DESeq2) more tedious, and the raw outputs don't make intuitive sense.

I just noticed that the aa-tRNA-seq reop uses a reference like the one I am proposing. So that's great but confusing.

https://github.com/rnabioco/aa-tRNA-seq/blob/main/ref/yeast.tRNAnanoref.wsplicing.dual.adapt.v2.fa