casts << {:long=>'kmer_max', :short=>'K', :type=>'uint', :mandatory=>true, :default=>31, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'cov_cutoff', :short=>'c', :type=>'list', :mandatory=>true, :default=>cov_cutoffs, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'exp_cov', :short=>'e', :type=>'float', :mandatory=>true, :default=>'auto', :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'clean', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'clean', :short=>'X', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
options = Biopieces.options_parse(ARGV, casts)