From 2021008d18ef8fcafc2380cf2538de144b0893b1 Mon Sep 17 00:00:00 2001
From: Cyriac Kandoth <ckandoth@gmail.com>
Date: Wed, 17 Feb 2016 18:57:53 -0500
Subject: [PATCH] Fix for when column to retain is not in input MAF

---
 maf2maf.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/maf2maf.pl b/maf2maf.pl
index 6bac10a..3885f4f 100644
--- a/maf2maf.pl
+++ b/maf2maf.pl
@@ -294,8 +294,8 @@
             else {
                 my $key = join( ":", map{ my $c = lc; $cols[$output_maf_col_idx{$c}] } qw( Chromosome Start_Position Tumor_Sample_Barcode Reference_Allele Tumor_Seq_Allele2 ));
                 foreach my $c ( map{lc} split( /\t/, $maf_header )){
-                    if( !$force_new_cols{$c} and defined $input_maf_data{$key}{$c} ) {
-                        $cols[$output_maf_col_idx{$c}] = $input_maf_data{$key}{$c};
+                    if( !$force_new_cols{$c} ) {
+                        $cols[$output_maf_col_idx{$c}] = ( defined $input_maf_data{$key}{$c} ? $input_maf_data{$key}{$c} : "" );
                     }
                 }
                 $tmp_tn_maf_fh->print( join( "\t", @cols ) . "\n" );