I am reading a file and storing the values in a hash.

Now, I am reading another file and storing the values in another hash. This file may contain the repeated values. So, I am checking the condition, if the key is already there and its value of 10th column is greater than the line which I am reading right now, than skip or replace it. I am getting output, sam as my input, without removing the repeated lines. What is wrong in my code?

use strict;
use warnings;

my $file1 = shift;
my $file2 = shift;

open (my $gene, $file1) || die "Can't open file $file1";                                

my %length;                                                                             

while (my $ge_line = <$gene>){                                                          
    chomp $ge_line;
    next if $ge_line =~ /^\#/;
    my @ge_split = split(/\t/, $ge_line);

    $length{$ge_split[5]} = $ge_split[8];                                           

}
close($gene);

my %seen;

open (my $tcga, $file2) || die "Can't open file $file2";                                

while (my $tc_line = <$tcga>){
    chomp $tc_line;
    next if $tc_line =~ /^\#/;

    my @tc_split = split(/\t/, $tc_line);

    next unless $tc_split[9] eq "syn";
    my $key = $tc_split[0]."-".$tc_split[1]."-".$tc_split[2]."-".$tc_split[3]."-".$tc_split[4]."-".$tc_split[5];

    my $my_len = $length{$tc_split[5]};

    unless ($my_len) {
        print STDERR "Could not find the length for $tc_split[5]\n" ;
        next;
    }

    if (exists $seen{$key}){
        my $a = $seen{$key};

        my @spl_a = split(/\t/, $a);

        if ($spl_a[10] > $my_len) {
            next;

        }else {
            $seen{$key} = $tc_line . "\t" . $my_len;
        }

    }else{
        $seen{$key} = $tc_line . "\t" .$my_len;
    }
}

foreach my $print(sort keys %seen){
    print $seen{$print} , "\n";
}

close ($tcga);