Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
input.each_with_index do |record, count|
- output.puts record unless options.has_key? :no_stream
+ output.puts record unless options[:no_stream]
$stderr.printf "\n% 9d ", count if (count % (options[:count] * 100)) == 0
$stderr.print "." if (count % options[:count]) == 0
end