From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 13 Jul 2012 14:15:39 +0000 (+0000)
Subject: fixed grave bug in find_orfs
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=5280e3f844606335557d7535ed33ffd8174469fd;p=biopieces.git

fixed grave bug in find_orfs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1870 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/find_orfs b/bp_bin/find_orfs
index 868665d..a1203ea 100755
--- 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