From a13d125ba15345a17ad8f4de5e7183493b2d0ea2 Mon Sep 17 00:00:00 2001
From: Menachem Fromer <fromer@broadinstitute.org>
Date: Thu, 7 Jun 2012 16:56:32 -0400
Subject: [PATCH] Split out contig names from Reference .fai file on white
 space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz,
 which does not use tab delimiters)

---
 public/perl/sortByRef.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/perl/sortByRef.pl b/public/perl/sortByRef.pl
index 71d3f4477..e17707796 100755
--- a/public/perl/sortByRef.pl
+++ b/public/perl/sortByRef.pl
@@ -50,7 +50,7 @@ my %ref_order;
 my $n = 0;
 while ( <DICT> ) {
     chomp;
-    my ($contig, $rest) = split "\t";
+    my ($contig, $rest) = split '\s';
     die("Dictionary file is probably corrupt: multiple instances of contig $contig") if ( defined $ref_order{$contig} );
 
     $ref_order{$contig} = $n;