Incorporate sequence > structure mapping step

[jayhesselberth]

Add a rule that takes tRNA sequences in FASTA format as input, and emits a Stockholmn alingment using cmalign from Infernal and the tRNA covariance model.

This alignment can then be used to align tRNA signals (e.g. base-calling error) to a common reference structure during visualization (e.g., a heatmap).