implemented rename
cleaned up Rename parser
Merge branch 'dev-rename' into dev
removed unused functions in FSeq
Functionalized grep implementation
implemented gff3 output functionality
Added reverse complement search option
Merged in new grep functionality from dev-biogrep
added IUPAC extended nucleotide code search option
Merge branch 'dev-grep' into dev
fixed bug in --count grep option
clarrified --count-matches grep help
made grep searches ignore case by default
updated docs
release 1.4.0
squashed deathbug in `smof grep -r --`
added --reverse-only and --both-strands options to grep
release 1.4.1