-casts << {:long=>'directory', :short=>'d', :type=>'dir', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'type', :short=>'t', :type=>'string', :mandatory=>true, :default=>'short', :allowed=>types, :disallowed=>nil}
-casts << {:long=>'kmer_min', :short=>'k', :type=>'uint', :mandatory=>true, :default=>19, :allowed=>nil, :disallowed=>nil}
-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}
-
-bp = Biopieces.new
+casts << {:long=>'directory', :short=>'d', :type=>'dir', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'type', :short=>'t', :type=>'string', :mandatory=>true, :default=>'short', :allowed=>types, :disallowed=>nil}
+casts << {:long=>'kmer_min', :short=>'k', :type=>'uint', :mandatory=>true, :default=>19, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'kmer_max', :short=>'K', :type=>'uint', :mandatory=>true, :default=>31, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'kmer_step', :short=>'s', :type=>'uint', :mandatory=>true, :default=>2, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'ins_length', :short=>'i', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'clean', :short=>'X', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}