require 'pp'
require 'maasha/biopieces'
require 'maasha/seq'
+require 'maasha/seq/backtrack'
+
+include BackTrack
casts = []
casts << {:long=>'forward', :short=>'f', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
input.each do |record|
- if record.has_key? :SEQ
+ if record[:SEQ]
forward = false
reverse = false
seq = Seq.new_bp(record)