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, counter_tab[i]); )
  }
  DEBUG( printf("OUT: %d\n", sum); )

  return sum;
}
 
##</code><code>##

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

##</code><code>##

...
__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 & 0xfffff); )

  return sum;
}