# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
casts = []
-bp = Biopieces.new
+options = Biopieces.options_parse(ARGV, casts)
-options = bp.parse(ARGV, casts)
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ if record.has_key? :SEQ and record.has_key? :ADAPTOR_POS
+ record[:SEQ] = record[:SEQ][0 ... record[:ADAPTOR_POS].to_i]
+ record[:SCORES] = record[:SCORES][0 ... record[:ADAPTOR_POS].to_i] if record[:SCORES]
+ record[:SEQ_LEN] = record[:SEQ].length
+ end
-bp.each_record do |record|
- if record.has_key? :SEQ and record.has_key? :ADAPTOR_POS
- record[:SEQ] = record[:SEQ][0 ... record[:ADAPTOR_POS].to_i]
- record[:SCORES] = record[:SCORES][0 ... record[:ADAPTOR_POS].to_i] if record[:SCORES]
- record[:SEQ_LEN] = record[:SEQ].length
+ output.puts record
end
-
- bp.puts record
end