refactoring slice_fasta_to_exons

slice_fasta_to_exons just returns the array of gene alignments.
more generically, slice_fasta_from_genbank_file does the same for any
type of locus.
refactoring, adding new features

refactored code so that all inputs make an array of alignments, then
output fasta file from that array depending on concat flag.
Added ability to specify coverage threshold and alt allele threshold