# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'sff'
+require 'maasha/biopieces'
+require 'maasha/sff'
casts = []
casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'mask', :short=>'m', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'clip', :short=>'c', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-bp = Biopieces.new
+options = Biopieces.options_parse(ARGV, casts)
-options = bp.parse(ARGV, casts)
-
-bp.each_record do |record|
- bp.puts record
-end
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ output.puts record
+ end
-num = 0
-last = false
-
-if options.has_key? :data_in
- options[:data_in].each do |file|
- SFF.open(file, mode='r') do |sff|
- sff.each do |entry|
- entry.mask if options[:mask]
- entry.clip if options[:clip]
- bp.puts entry.to_bp
- num += 1
-
- if options.has_key? :num and options[:num] == num
- last = true
- break
+ num = 0
+ last = false
+
+ if options[:data_in]
+ options[:data_in].each do |file|
+ SFF.open(file, mode='r') do |sff|
+ sff.each do |entry|
+ entry.mask if options[:mask]
+ entry.clip if options[:clip]
+ output.puts entry.to_bp
+ num += 1
+
+ if options[:num] and options[:num] == num
+ last = true
+ break
+ end
end
end
- end
- break if last
+ break if last
+ end
end
end