Assuming the strings are fairly short and contain a limited number of unique characters, which is likely in this case:

print diffCount('aaaaacaacaaagcc', 'acaggtgacaaaaaa');

sub diffCount {
    my (%counts, $sum, $i);

    $counts{substr($_[0], $_, 1)}++ for 0..(length($_[0]) - 1);
    $counts{substr($_[1], $_, 1)}-- for 0..(length($_[1]) - 1);

    $sum += abs $_ for values %counts;

    return $sum;
}

[download]

I tried other methods using split, regex, etc., but this benchmarked the fastest. Obviously, doing the same thing in C or C++ would be even faster.

In reply to Re: The sum of absolute differences in the counts of chars in two strings. by TJPride
in thread The sum of absolute differences in the counts of chars in two strings. by BrowserUk

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