X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fread_sff;h=3de8b2ea1afea9e5a7e9213eac4913e8b7a01f01;hb=d5a8efe4d822a139b452bd35e2353aaccd84ac4c;hp=6e5febd247175040751cee158fa9123949ff6bbc;hpb=494dc53ebd515b1e3e9b91bbebf43059899ca4ce;p=biopieces.git

diff --git a/bp_bin/read_sff b/bp_bin/read_sff
index 6e5febd..3de8b2e 100755
--- a/bp_bin/read_sff
+++ b/bp_bin/read_sff
@@ -37,34 +37,34 @@ casts << {:long=>'num',     :short=>'n', :type=>'uint',   :mandatory=>false, :de
 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.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]
+          output.puts entry.to_bp
+          num += 1
+
+          if options.has_key? :num and options[:num] == num
+            last = true
+            break
+          end
         end
       end
-    end
 
-    break if last
+      break if last
+    end
   end
 end