Mavericks suggestion to set the input record separator to 0x0c will allow you to read in one record at a time and avoid all that mucking around with single characters. It will no doubt speed your code considerably as well as simplifying it quite a lot. Let Perl work for you.

Here is a small optimisation of your last two subs that will save a bit of time too. By using the 'x' operator rather than a while loop we add our whitespace pad in one operation. By using a regex to stip leading and trailing whitespace we save a lot of mucking about and let the regex engine do the work. This too will be much faster.

# Pad out with trailing whitespace as necessary
sub pad {
    my ($data, $len) = @_;
    my $pad = $len - (length $data);
    $data .= " " x $pad unless $pad < 0;
  return $data;
}

# Get rid of leading/trailing whitespace
sub normalise {
    my $value = shift;
    $value = s/^\s+|\s+$//gm;
  return $value;
}
[download]

Hope this helps

cheers

tachyon

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