fixed isseu in find_orphans

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2207 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/find_orphans b/bp_bin/find_orphans
index d8f2e4e6d8f80784618b4af1d8761c67d24447ae..20cc9c27a5dc2ff74e193c1e18551567547bd886 100755 (executable)
--- a/bp_bin/find_orphans
+++ b/bp_bin/find_orphans
@@ -24,7 +24,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# Identify paired end orphan in records with sequence data.
+# Find paired end orphan in records with sequence data.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -48,22 +48,24 @@ records = []
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
-    records << record
+    if record[:SEQ_NAME]
+      records << record
 
-    if records.size == 2
-      if Illumina.name_match?(records.first[:SEQ_NAME], records.last[:SEQ_NAME])
-        records.first[:TYPE] = "paired"
-        records.last[:TYPE]  = "paired"
+      if records.size == 2
+        if Illumina.name_match?(records.first[:SEQ_NAME], records.last[:SEQ_NAME])
+          records.first[:TYPE] = "paired"
+          records.last[:TYPE]  = "paired"
 
-        output.puts records.first
-        output.puts records.last
+          output.puts records.first
+          output.puts records.last
 
-        records = []
-      else
-        records.first[:TYPE] = "orphan"
-        output.puts records.first
+          records = []
+        else
+          records.first[:TYPE] = "orphan"
+          output.puts records.first
 
-        records.shift
+          records.shift
+        end
       end
     end
   end