commands << "-j #{@infile2}"
commands << "-o #{@outfile}"
commands << "-p #{@program}"
+ commands << "-W #{options[:word_size]}" if options[:word_size]
commands << "-D 1" # tabular output
commands << "-e #{options[:e_val]}"
commands << (options[:megablast] ? "-m T" : "-m F")
casts << {:long=>'filter', :short=>'f', :type=>'string', :mandatory=>false, :default=>'no', :allowed=>'yes,no', :disallowed=>nil}
casts << {:long=>'megablast', :short=>'m', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'no_gaps', :short=>'G', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'word_size', :short=>'w', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
options = Biopieces.options_parse(ARGV, casts)