Create GMT::Analysis::Maf and refactor methods into it

code-deduplication: jweible
Remove useless comments

code-deduplication: jweible
cleanup
Switch IUB method to tolerate translating 'U' to 'T'

Refactors to use Genome::Infor::IUB failed to account for the fact that the
original method accepted 'U.'  Consultation with Dave Larson lead us to believe
that these should not pollute the original IUB functionality, so a new 'rna_safe'
version of the method was created, and things that used the original were
switched over.