Constrain the outgoing reference bases alphabet to ACTGN

A repository may be lenient in the data they accept at import-time, but should be strict in what they emit at serving-time.
It's fairly common to align reads to transcripts (e.g., with [tophat](https://docs.google.com/document/d/1t1gi2Djxd0ykMVe2bF8BVOBsOsPngjFh2999u3rZq-A/edit?hl=en&authkey=CKL1i8sD)), although I guess that they're just using a sliced version of reference contigs. The GATK can call variants with RNA-seq data. I don't know though if they do anything special with T/U here though? I'm not familiar enough with those workflows...