fixed grave bug in find_orfs

[biopieces.git] / bp_bin / find_orfs

diff --git a/bp_bin/find_orfs b/bp_bin/find_orfs
index 868665da2a1305683845171934056ac6f4523f4e..a1203ead90735803f94eb22e91d2af9e1e3673d6 100755 (executable)
--- a/bp_bin/find_orfs
+++ b/bp_bin/find_orfs
@@ -37,12 +37,14 @@ casts << {:long=>'start_codons',  :short=>'s', :type=>'list', :mandatory=>true,
 casts << {:long=>'stop_codons',   :short=>'S', :type=>'list', :mandatory=>true,  :default=>"UAA,UGA,UAG", :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'min_size',      :short=>'m', :type=>'uint', :mandatory=>true,  :default=>50,            :allowed=>nil, :disallowed=>'0'}
 casts << {:long=>'max_size',      :short=>'M', :type=>'uint', :mandatory=>true,  :default=>10_000,        :allowed=>nil, :disallowed=>'0'}
-casts << {:long=>'non_redundant', :short=>'r', :type=>'flag', :mandatory=>false, :default=>nil,           :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'non_redundant', :short=>'n', :type=>'flag', :mandatory=>false, :default=>nil,           :allowed=>nil, :disallowed=>'0'}
 
 options = Biopieces.options_parse(ARGV, casts)
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
+    output.puts record
+
     if record[:SEQ]
       entry = Seq.new_bp(record)
 
@@ -55,11 +57,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 
         output.puts new_record
       end
-
-      exit
     end
-
-    output.puts record
   end
 end