Guys,
I want to use bitwise XOR operator which is known to be fast for bitwise testing. What I intend to do below is to find number of matching positions (except N matching is not counted).
my $s1 = "STCATTNNNSATCGCT"; 
my $s2 = "ATCGTCGSNNNNATCG";
           ## #   0     #

# There are 4 matching positions - marked with (#) -
# and notice that matching N is not counted (0)

[download]
My best attempt with it is this, which leads me nowhere. 
my $match = $s1 ^ $s2;
my $match_count = $match =~ tr/\00//;
print "$match_count\n";

# This gives 5, because N is counted.
# How can I make it to return 4 instead?

[download]
Because the code I have below - using subscripted for loop - already does its job, but it is horribly slow: 

get_match_count($s1,$s2);

sub get_match_count {

    my ( $k, $l ) = @_;
    return 0 if $k eq $l;

    my $len       = length($k);
    my $num_match = 0;

    for ( my $i = 0; $i < $len; $i++ ) {
        next if ( substr( $k, $i, 1 ) eq 'N' 
                        and 
                  substr( $l, $i, 1 ) eq 'N' );
        ++$num_match if substr( $k, $i, 1 ) eq substr( $l, $i, 1 );
    }

    print "$num_match\n";
    return $num_match;
}

[download]

Regards,
Edward

In reply to Conditional Bitwise XOR(^) Operator in Matching Chars Count of Two Strings? by monkfan

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