updated order_pairs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1855 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/order_pairs b/bp_bin/order_pairs
index e8f799052470feb9dd6bfb3eac9a8cd706ea55d5..395b8fe37d643553dcda07d5e973b3952251e452 100755 (executable)
--- a/bp_bin/order_pairs
+++ b/bp_bin/order_pairs
@@ -47,11 +47,13 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
         name = $1.to_sym
         pair = $2.to_i
       else
-        $stderr.puts "WARNING: Unmatched sequence name: #{record[:SEQ_NAME]}" if options[:verbose]
+        $stderr.puts "WARNING: Unmatched sequence name: #{record[:SEQ_NAME]}"
       end
 
       if pair == 1
         if hash2[name]
+          record[:ORDER]      = "paired"
+          hash2[name][:ORDER] = "paired"
           output.puts record
           output.puts hash2[name]
 
@@ -61,6 +63,8 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
         end
       elsif pair == 2
         if hash1[name]
+          hash1[name][:ORDER] = "paired"
+          record[:ORDER]      = "paired"
           output.puts hash1[name]
           output.puts record
 
@@ -71,13 +75,19 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
       end
     end
   end
-end
 
-if options[:verbose]
-  $stderr.puts "Unmatched names with 1st read pair: #{hash1.size}"
-  $stderr.puts "Unmatched names with 2nd read pair: #{hash2.size}"
+  hash1.each_value do |record|
+    record[:ORDER] = "orphan 1"
+    output.puts record
+  end
+
+  hash2.each_value do |record|
+    record[:ORDER] = "orphan 2"
+    output.puts record
+  end
 end
 
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<