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;
[download]

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;
[download]

why can't i use dnacmp2? it seems to work just fine with the above code

why can't i use dnacmp2? it seems to work just fine with the above code

As I mentioned above, dnacmp() produces a list of mismatches, (Eg. "1:A:C", "2:A:G").

So in the first version of the counting code I posted:

m[\d+:(.:.)] and ++$stats{ $1 } for dnacmp( @seqs[ $i, $j ] );
[download]

I iterate over that list (using for), and m///atch against each individual mismatch in order to count.

But dnacmp2 returns a single string containing all the mismatches, (Eg. "1:A:C 2:A:G"), so the above method would only see and count the first mismatch.

In the latest code, I use:

++$stats{ $1 } while $res =~ m[:(.:.)]g;
[download]

Which uses a while loop and m///g to count all the mismatches in the single string.

---

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

The start of some sanity?