removed debug message

[biopieces.git] / bp_bin / order_pairs

diff --git a/bp_bin/order_pairs b/bp_bin/order_pairs
index c96f845f63b14b7a62e5c699fff895562949e626..395b8fe37d643553dcda07d5e973b3952251e452 100755 (executable)
--- a/bp_bin/order_pairs
+++ b/bp_bin/order_pairs
@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 
-# Copyright (C) 2007-2011 Martin A. Hansen.
+# Copyright (C) 2007-2012 Martin A. Hansen.
 
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
@@ -24,11 +24,10 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# Order records so SEQ_NAME/1 and SEQ_NAME/2 are in order.
+# Order records with pair end sequence data.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-
 require 'maasha/biopieces'
 require 'pp'
 
@@ -40,11 +39,21 @@ hash2 = {}
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
     if record[:SEQ_NAME]
-      name = record[:SEQ_NAME][0 ... -2].to_sym
-      pair = record[:SEQ_NAME][-1].to_i
+      case record[:SEQ_NAME]
+      when /^(.+)\/(\d)$/   # Illumina 1.5
+        name = $1.to_sym
+        pair = $2.to_i
+      when /^(.+) (\d):/    # Illumina 1.8
+        name = $1.to_sym
+        pair = $2.to_i
+      else
+        $stderr.puts "WARNING: Unmatched sequence name: #{record[:SEQ_NAME]}"
+      end
 
       if pair == 1
-        if hash2.has_key? name
+        if hash2[name]
+          record[:ORDER]      = "paired"
+          hash2[name][:ORDER] = "paired"
           output.puts record
           output.puts hash2[name]
 
@@ -53,7 +62,9 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
           hash1[name] = record
         end
       elsif pair == 2
-        if hash1.has_key? name
+        if hash1[name]
+          hash1[name][:ORDER] = "paired"
+          record[:ORDER]      = "paired"
           output.puts hash1[name]
           output.puts record
 
@@ -61,16 +72,19 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
         else
           hash2[name] = record
         end
-      else
-        $stderr.puts "WARNING: Badly formatted name: #{record[:SEQ_NAME]}" if options[:verbose]
       end
     end
   end
-end
 
-if options[:verbose]
-  $stderr.puts "Unmatched names with /1: #{hash1.size}"
-  $stderr.puts "Unmatched names with /2: #{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