ok, i think inline::c is a little beyond me. i'm trying it out with the following code:

# V5: Inline::C
#!/opt/local/bin/perl
use strict;
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;

my $bamfile = Bio::DB::Sam->new( -bam => "eg1.bam" );
my @allReads = $bamfile->features( -type => 'match' );
for my $read (@allReads) {
    ( $ref, $matches, $query ) = $read->padded_alignment;
    print $read->qname, "\n", dnacmp2('$ref', '$query');
}
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first, i extract some information from the .bam file. then, i create the target and the test sequence on the fly in the subsequent for loop. $ref represents the target and $query represents the test (both are just strings). i then try to feed these two variables into dnacmp2 and print a few more things before it ($read->qname represents a sequence identifier), but it throws the following error:

Global symbol "$query" requires explicit package name at mutations.pl 
+line 133.
Execution of mutations.pl aborted due to compilation errors.
Pradeep-Bandarus-MacBook-Pro:test pradeepbandaru$ perl mutations.pl
Global symbol "$ref" requires explicit package name at mutations.pl li
+ne 133.
Global symbol "$matches" requires explicit package name at mutations.p
+l line 133.
Global symbol "$query" requires explicit package name at mutations.pl 
+line 133.
Execution of mutations.pl aborted due to compilation errors.
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