Fix for when column to retain is not in input MAF

mskcc · Apr 8, 2016 · 2021008 · 2021008
1 parent 8f0d6bc
commit 2021008
Showing 1 changed file with 2 additions and 2 deletions.
diff --git 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" );