I have a directory of text files and I want to process each file in that directory using the subroutine average to calculate the average for a file. However, my script processes the same file every time. I am not sure what is the mistake I am doing here. Below is the code I wrote:

#!/usr/bin/perl
#Naga_betrapally_6_3_16
use strict;
use warnings;
use Cwd;
use FileHandle;
my $name;                                                             
+                    # Naming of variables, remembers the name of the 
+file
my $cwd = getcwd();                                                   
+                   #Takes in the current directory of files
my $opendir = "$cwd";                                                 
+                  #Used to open the current directory and remembers t
+he location
opendir (DIR, $opendir) or die $!;                                    
+                  #Open directory command
my @directory = readdir DIR;                                          
+                   #Grabbing all the fas files stored in the location
my $scalar = scalar(@directory);                                      
+                  #Counting the number of files and printing it in th
+e next line
#print "The number of sample files in this folder: $scalar \n";
# for (my $i=0; $i<scalar(@directory); $i++){
# $name = "$directory[$i]";
# print "The file read in: $name\n";
# my $digits = substr $name, 0, 4;                                    
+                  #Grabbing the first 4 characters to name the sample
+ run for MEGA
# my $tmp = "$opendir/$directory[$i]";

# }

for(my$i=0;$i<@directory;$i++){
print $directory[$i];
&average($directory[$i]);
}

 #average(@directory);

sub average {
my $header;
my @array_lines;
my $n=0;
my $filename=@_;                                                      
+                       #Takes in the sequence file from the user inpu
+t with the year in the header
my @average_array;
my $sum =0;
my $avarage;
     next if($filename =~ /^\.$/);
     next if($filename =~ /^\.\.$/);
open (FILE,$filename) or die "No input file provided or the input file
+ does not exist in the path, '$_' $!";
print "$filename\n";
while (my $file = <FILE>){
chomp $file;
if ($file =~/^Name/){
$header = $file;
}
else{
$array_lines[$n] = $file;  
chop $array_lines[$n];
$n++;
}
}                    
for(my $i=0;$i<@array_lines;$i++){
my @tmp = split(/\t/,($array_lines[$i]));
#print $tmp[3];
push @average_array, $tmp[3];
my $scalar = scalar(@average_array);
#print $scalar;
}    
foreach (@average_array){
    #print "$_\n";
    my $tmp = $_;
    $tmp =~ s/,//;
    #print "$tmp\n";
    $sum = $sum+$tmp;
    }    
#print "The sum of all the mapping is $sum\n";
$avarage = $sum/11;
#print "THe average of the mapping is $avarage\n";
close (FILE);
}
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All the files in that folder maintain the same structure as the sample file below:

Name    Consensus length    Total read count    Average coverage    Re
+ference sequence    Reference length
NSP4-E1 mapping    750    227760    64,516.84    NSP4-E1    750
VP7-G3 mapping    1062    303758    63,062.33    VP7-G3    1062
Rotarix-VP6 mapping    1356    161491    26,020.50    Rotarix-VP6    1
+356
Rotarix-NSP1 mapping    1559    114394    16,077.21    Rotarix-NSP1   
+ 1568
NSP2-N1 mapping    1059    80424    16,178.61    NSP2-N1    1058
NSP5-H1 mapping    664    75269    23,943.71    NSP5-H1    663
VP1-R1 mapping    3302    69677    4,542.15    VP1-R1    3302
VP2-C1 mapping    2717    149312    11,987.00    VP2-C1    2717
VP3-M1 mapping    2591    31795    2,632.39    VP3-M1    2591
RotaTeq-WI79-4-VP4 mapping    2359    78305    7,223.08    RotaTeq-WI7
+9-4-VP4    2359
NSP3-T1 mapping    1074    173210    34,910.87    NSP3-T1    1074
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