#!/usr/bin/perl
use strict;
use warnings;
use App::Fasops;

App::Fasops->run;

=head1 OVERVIEW

For help with App::Fasops, run "fasops help"

=cut

__END__

perl -I lib/ script/fasops

perl -I lib/ script/fasops names t/example.fas -c -o stdout

perl -I lib/ script/fasops subset t/example.fas t/example.name.list -o stdout

perl -I lib/ t/04-subset.t

perl -I lib/ script/fasops separate t/example.fas --nodash --rc
perl -I lib/ script/fasops separate t/example.fas --nodash --rc -o stdout

perl -I lib/ script/fasops covers t/example.fas -o stdout -n S288c

perl -I lib/ script/fasops axt2fas t/example.axt -o stdout
perl -I lib/ script/fasops maf2fas t/example.maf -o stdout

perl -I lib/ script/fasops links t/example.fas -o stdout
perl -I lib/ script/fasops replace t/example.fas t/replace.tsv -o stdout

perl -I lib/ script/fasops refine t/example.fas --msa mafft -o stdout

perl -I lib script/fasops slice t/slice.fas t/slice.yml --name S288c

perl -I lib script/fasops join t/S288cvsRM11_1a.slice.fas t/S288cvsYJM789.slice.fas t/S288cvsSpar.slice.fas -n S288c -o stdout
