-class Pattern
- def initialize(options)
- @options = options
- @patterns = []
- @patterns << pattern_internal
- @patterns += patterns_end if @options[:partial]
- end
-
- def to_i
- new_patterns = []
-
- while @patterns.size > 1
- new_patterns = @patterns[0 ... -2]
- new_patterns << "( #{@patterns[-2 .. -1].join(' | ')} )"
+casts = []
+casts << {:long=>'forward', :short=>'f', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'forward_rc', :short=>'F', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'reverse', :short=>'r', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'reverse_rc', :short=>'R', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'len_forward', :short=>'l', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'len_reverse', :short=>'L', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'mismatches', :short=>'m', :type=>'uint', :mandatory=>false, :default=>10, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'insertions', :short=>'i', :type=>'uint', :mandatory=>false, :default=>5, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'deletions', :short=>'d', :type=>'uint', :mandatory=>false, :default=>5, :allowed=>nil, :disallowed=>nil}