$out[45] = "VUS";

print OF join("\t",@out),"\n";

#!/bin/perl

use strict;

my %nms=("NM_004004.5"=>"AR","NM_004992.3"=>"XLD","NM_003924.3"=>"AD");
my $input_file = $ARGV[0];
my $output_file = $ARGV[1];

my @left =  (
     "Index",
     "Chromosome Position",
     "Gene",
     "Inheritance",
     "RNA Accession",
     "Chr",
     "Coverage",
     "Score",
     "A(#F,#R)",
     "C(#F,#R)",
     "G(#F,#R)",
     "T(#F,#R)",
     "Ins(#F,#R)",
     "Del(#F,#R)",
     "SNP db_xref",
     "Mutation Call",
     "Mutant Allele Frequency",
     "Amino Acid Change"
 );
my @right = (
    "HP",
    "SPLICE",
    "Pseudogene",
    "Classification",
    "HGMD",
    "Disease",
    "Sanger",
    "References"
);

my $final_header;
open (FH, "<", $input_file) or die "Can't open $input_file: $!";
chomp(my $hdr=<FH>);
$final_header = sprintf("%s\t%s\t%s\n", join("\t", @left), $hdr, join("\t",@right));

open (OF, ">", $output_file) or die "Can't open $output_file: $!";
print OF "$final_header";

my @colsleft = map "Null",(1..$#left);
print "\@colsleft = ", scalar @colsleft, ": @colsleft\n";

my @colsright = map "Null",(0..$#right);
print "\@colsright = ", scalar @colsright, ": @colsright\n";

while(<FH>)  {
chomp;
my @vals = split/\t/;
my @mutations=split/,/,$vals[9];
my ($gene,$transcript,$exon,$coding,$aa);
for (@mutations)
{
    $_ or next;
    ($gene,$transcript,$exon,$coding,$aa) = split/\:/; # this takes col AB and splits it at colons

    grep {$transcript eq $_} keys %nms or next;
}
my @out=($.,@colsleft,$_,@colsright);
print "\n";
print 'After this evaluation: my @out=($.,@colsleft,$_,@colsright);', "\n";
print "\@out = ", scalar @out, ": @out\n\n";

$out[2]=$gene;
$out[3]=$nms{$transcript};
$out[4]=$transcript;
$out[15]=$coding;
$out[17]=$aa;
$out[45] = "VUS";

print 'After this evaluation:  $out[45] = "VUS";', "\n";
print "\@out = ", scalar @out, ": @out\n\n";

print OF join("\t",@out),"\n";

my @after = split( "\t", join("\t", @out) );
print "\@after = ", scalar @after, ": @after\n";
}

perl debug.pl input.file /dev/null

@colsleft = 17: Null Null Null Null Null Null Null Null Null Null Null Null Null Null Null Null Null
@colsright = 8: Null Null Null Null Null Null Null Null

After this evaluation: my @out=($.,@colsleft,$_,@colsright);
@out = 27: 2 Null Null Null Null Null Null Null Null Null Null Null Null Null Null Null Null Null 4     41748130        41748130        G       C       exonic  PHOX2B      synonymous SNV   PHOX2B:NM_003924.3:exon3:c.C639G:p.G213G        0.0007  .       .       .       .       .       0.0005  0.0002  0.0007  . Null Null Null Null Null Null Null Null

After this evaluation:  $out[45] = "VUS";
@out = 46: 2 Null PHOX2B AD NM_003924.3 Null Null Null Null Null Null Null Null Null Null c.C639G Null p.G213G 4        41748130        41748130        G       C       exonic       PHOX2B          synonymous SNV  PHOX2B:NM_003924.3:exon3:c.C639G:p.G213G        0.0007  .       .       .       .       .       0.0005  0.0002  0.0007  . Null Null Null Null Null Null Null Null                   VUS

@after = 65: 2 Null PHOX2B AD NM_003924.3 Null Null Null Null Null Null Null Null Null Null c.C639G Null p.G213G 4 41748130 41748130 G C exonic PHOX2B  synonymous SNV PHOX2B:NM_003924.3:exon3:c.C639G:p.G213G 0.0007 . . . . . 0.0005 0.0002 0.0007 . Null Null Null Null Null Null Null Null                   VUS