Here's my brute-force try. Don't know if the call-overhead is bigger than the gain? I assumed a one-byte-is-one-character relationship (no wchar's yet). HTH 

use Inline C;
use strict;
use warnings;
use Time::HiRes qw(time);

my $str1 = "abcdefabc";
my $str2 = "xyzabcabc@@@";

my $now = time;
my $res;

$res = deltasum( $str1, $str2 ) for (1..1_000_000);
print "res=$res   time=",  ( time() - $now ), "us\n";
#res=9   time=0.819153070449829us

__END__

__C__

#define DEBUG(x) 

int counter_tab[256];

int deltasum(char* a, char* b) {
  int i;
  int sum = 0;

  DEBUG( printf("IN: (%d:%s) (%d:%s)\n", strlen(a), a, strlen(b), b); 
+)

  bzero( counter_tab, sizeof( counter_tab ) );
  for ( ; *a ; ++a ) ++counter_tab[ *a ];
  for ( ; *b ; ++b ) --counter_tab[ *b ];

  for ( i = 0; i < 256; ++i ) { /* maybe reduced to significant range?
+ */
    sum += abs( counter_tab[i] );
    DEBUG( if ( counter_tab[i] ) printf( "'%c' (%3d) x %5d\n", i, i, c
+ounter_tab[i]); )
  }
  DEBUG( printf("OUT: %d\n", sum); )

  return sum;
}

[download]
Update: Moved i and sum to head of function to cope with ancient compilers (thanks to davido). Simplified sizeof() expression.

Debug sample: 

IN: (9:abcdefabc) (12:xyzabcabc@@@)
'@' ( 64) x    -3
'd' (100) x     1
'e' (101) x     1
'f' (102) x     1
'x' (120) x    -1
'y' (121) x    -1
'z' (122) x    -1
OUT: 9

[download]

Update: Approx. 60% speed-up when limiting to [ACGTacgt], still room for improvement... 

...
__END__

__C__

#define DEBUG(x)
#define GATTACA(x)  (x)=='A' || (x)=='C' || (x)=='G' || (x)=='T' || \
                    (x)=='a' || (x)=='c' || (x)=='g' || (x)=='t'

int deltasum_acgt(char* a, char* b) {
  int i;
  int sum     = 0;
  int tab[8]  = {0};
  int ignored = 0;

  DEBUG( printf("IN (%d:%s) (%d:%s)!\n", strlen(a), a, strlen(b), b); 
+)

  for ( ; *a ; ++a ) {
    if ( GATTACA( *a  ) ) ++tab[ *a & 0x07 ];
    else ++ignored;
  }

  for ( ; *b ; ++b ) {
    if ( GATTACA( *b ) ) --tab[ *b & 0x07 ];
    else ++ignored;
  }

  sum += abs( tab[1] ); /* A */
  sum += abs( tab[3] ); /* C */
  sum += abs( tab[7] ); /* G */
  sum += abs( tab[4] ); /* T */
  sum += ignored << 20; /* signal ill chars */

  DEBUG( for (i=0; i<7; ++i) printf("%d -> %d\n", i, tab[i]); )
  DEBUG( printf("OUT: %d  ign=%d delta=%d\n", sum, ignored, sum & 0xff
+fff); )

  return sum;
}

[download]
Script shall mask ignored characters from returned value by using $delta = $res & 0xfffff;. Number of chars ignored is $ign = $res >> 20; (think system / $?).
Assumption: Maximum number of differences is not much more than one million.

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

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