[Feature]: Add ability to use files as a reference genome

[MillironX]

Summary

Allow using FASTA files as reference genomes.

Added Features

Additional Changed parameters

If a file is passed to the --genome parameter or referenced from an entry in the --genome_list, then use it as a genome. The parameter should be of the form FILE:CHROMOSOME.

More Info

Context

This would make it easier to use YAVSAP on more exotic viruses that might not have GenBank entries, or to flesh out less complete GenBank records.