i don't get the output though...is it a Data::Dump problem?

Hm. Dunno. Are you redirecting the output to a file via the command line? If so, then you may have missed that by default, pp sends its output to STDERR not STDOUT.

If you want it redirected to the same file as the other output, then you should use print pp \%stats;

But if that is not the problem, then you can substitute this for the pp \%stats;

print "$_ => $stats{ $_ }" for sort keys %stats;
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Also, you should be using dnacmp() not dnacmp2 with the counting code I posted.

However, that means you are processing each string twice, once to count and once for printing, and that's just doubling your runtime.

Try this instead:

#!/opt/local/bin/perl
use Inline C => Config => BUILD_NOISY => 1;
use Inline C => <<'END_C', NAME => 'dnacmp', CLEAN_AFTER_BUILD => 0;

void dnacmp( char *a, char *b ) {
    int n = 0;
    Inline_Stack_Vars;

    Inline_Stack_Reset;
    while( *a && *b ) {
        if( *a != *b ) {
            Inline_Stack_Push( sv_2mortal( newSVpvf( "%d:%c:%c", n, *a
+, *b ) ) );
        }
        a++; b++; n++;
    }
    Inline_Stack_Done;
    return;
}

SV *dnacmp2( char *a, char *b ) {
    SV *res = newSVpv( "", 0 );
    int n = 0;

    while( *a && *b ) {
        if( *a != *b )
            sv_catpvf( res, "%d>%c:%c ", n, *a, *b );
        ++a, ++b, ++n;
    }
    return res;
}
END_C

use Bio::Seq;
use Bio::DB::Sam;
use Data::Dump qw[ pp ];

my $bamfile = Bio::DB::Sam->new( -bam => "eg1.bam" );
my @allReads = $bamfile->features( -type => 'match' );
my %stats;

for my $read (@allReads) {
    my ( $ref, $matches, $query ) = $read->padded_alignment;
    my $res = dnacmp2( $ref, $query );
    ++$stats{ $1 } while $res =~ m[:(.:.)]g;
    print $read->qname, "\n", $res, "\n";
}
print pp \%stats;
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