From 17d204335440c315b05df2f41984524e4be30e14 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 23 Jun 2010 20:59:38 +0000
Subject: [PATCH] bug fix: now contigs not present in the sequence dictionary
 are registered properly and do not cause the script to break

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3623 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/sortByRef.pl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/perl/sortByRef.pl b/perl/sortByRef.pl
index 7f7038f20..71d3f4477 100755
--- a/perl/sortByRef.pl
+++ b/perl/sortByRef.pl
@@ -86,6 +86,7 @@ while ( <$INPUT> ) {
     my $order;
     if ( defined $ref_order{$contig} ) { $order = $ref_order{$contig}; }
     else {
+        $ref_order{$contig} = $n;
         $order = $n; # input line has contig that was not in the dict; 
         $n++; # this contig will go at the end of the output, 
               # after all known contigs