In the above code, you are limited to the length of the shortest file. Instead, you can read each line separately into a hash with the key being the line number. You can do a single pass comparison for the same key in each hash.
Example:
# read in file one and place into a hash
my $line_number = 1;
while ( <$infile1> ) {
chomp;
$hash1{$line_number} = $_;
$line_number++;
}
# read in file 2 and place in a hash
$line_number = 1;
while (<$infile2>) {
chomp;
$hash2{$line_number) = $_;
$line_number++;
}
# determine the file with the largest number of keys
my @keys1 = keys %hash1;
my @keys2 = keys %hash2;
my $NoK1 = @keys1;
my $NoK2 @keys2;
if ($NoK1 > $NoK2) {
for $key (sort {$a <=> $b} keys %hash1) {
if (!defined $hash2{$key}) {
next;
}
elsif ($hash1{$key} eq $hash2{$key}) {
#do nothing?
next;
}
else {
print "Line number $key in both files is different";
}
}
# the rest of the code you can figure out from here
...
Hope that helps!