From 1b16b35d69028d04aa5a7168fe92d16ff4741d45 Mon Sep 17 00:00:00 2001
From: Cyriac Kandoth <ckandoth@gmail.com>
Date: Thu, 8 Feb 2018 14:28:26 -0500
Subject: [PATCH] Fix tabs for empty MAF columns before newline

---
 vcf2maf.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/vcf2maf.pl b/vcf2maf.pl
index 24851c2..4bb2cf6 100644
--- a/vcf2maf.pl
+++ b/vcf2maf.pl
@@ -839,7 +839,7 @@ sub GetBiotypePriority {
 
     # If there are additional INFO data to add, then add those
     foreach my $info_col ( @addl_info_cols ) {
-        $maf_line{$info_col} = ( $info{$info_col} ? $info{$info_col} : "" );
+        $maf_line{$info_col} = ( defined $info{$info_col} ? $info{$info_col} : "" );
     }
 
     # If this is an SV, pair up gene names from separate lines to backfill the Fusion column later
@@ -882,7 +882,7 @@ sub GetBiotypePriority {
         }
         else {
             # Write the gene-pair name into the Fusion column if it was backfilled earlier
-            my @cols = split( /\t/, $line );
+            my @cols = split( /\t/, $line, -1 );
             my $sv_key = $cols[$var_id_idx] . "-" . $cols[$tid_idx];
             $cols[$fusion_idx] = $sv_pair{$sv_key} if( $sv_pair{$sv_key} );
             $out_maf_fh->print( join( "\t", @cols ) . "\n" );