my $n = 0;
open(TEMP1, $overlap_files[$i]) || die "\n\nCan't open $overlap_files[$i]!!\n\n";
my $n = 0;
my @file1;
$file1[ $n++ ] = $_ while <TEMP1>;
close TEMP1;

open(TEMP2, $overlap_files[$j]) || die "\n\nCan't open $overlap_files[$j]!!\n\n";
$n = 0;
my @file2
$file2[ $n++ ] = $_ while <TEMP2>;
close TEMP2;