Here's the code I mentioned in my previous post. The 'add' function works properly if I execute it, whereas calling 'doSSW' results in a "Undefined subroutine" error. Thus my guess is that the issue lies with passing Perl strings to a C++ function.

#!/usr/bin/perl
use warnings;
use Inline CPP => Config => BUILD_NOISY => 1, CLEAN_AFTER_BUILD => 0;
use Inline CPP => Config => AUTO_INCLUDE => '#include "ssw_cpp.h"';
use Inline CPP;

my $ref = "CAGCCTTTCTGACCCGGAAATCAAAATAGGCACAACAAA";
my $seq = "CTGAGCCGGTAAATC";

print add(3,5)."\n";

my $returned = cprintit($seq);
print $returned."\n";

#my $cigar = do_SSW($seq,$ref);
#print "$cigar\n";

__END__
__CPP__

using namespace std;
string do_SSW(const char* queryC, const char* refC) {
    Inline_Stack_Vars;
    string query(queryC);
    string ref(refC);
    StripedSmithWaterman::Aligner aligner;
    StripedSmithWaterman::Filter filter;
    StripedSmithWaterman::Alignment alignment;
    aligner.Align(query.c_str(), ref.c_str(), ref.size(), filter, &ali
+gnment);
    return alignment.cigar_string;
}

int add (const int a, const int b) {
    int c = a+b;
    return c;
}

int cprintit(const string seq) {
    cout << seq << endl;
    return 10;
}
[download]

Thus my guess is that the issue lies with passing Perl strings to a C++

I think it might have more to do with the way that the string has been passed.
For example, cprintit() works fine if you rewrite it as:

int cprintit(const char * seq) {
    cout << seq << endl;
    return 10;
}
[download]

That's how you've passed the strings to do_SSW() - the problem with do_SSW() is that you've specified a *return* of type "string".
Perl's typemapping doesn't handle passing of the "string" type (either as argument or as return). You'll need to provide a typemap for "string" if you want to pass that type around.
What happens if you specify a return type of "char *" (instead of "string") for do_SSW() ?

For a solution using a typemap, this works for me:

#!/usr/bin/perl
use warnings;
use Inline CPP => Config => BUILD_NOISY => 1,
 TYPEMAPS => 'C:/_32/pscrpt/inline-cpp/stringtype.map',
 CLEAN_AFTER_BUILD => 0;

use Inline CPP;

my $seq = "CTGAGCCGGTAAATC";


my $returned = cprintit($seq);
print $returned."\n";


__END__
__CPP__

using namespace std;


int cprintit(string seq) {
    cout << seq << endl;
    return 10;
}
[download]

where 'C:/_32/pscrpt/inline-cpp/stringtype.map' contains the following single line (plus newline):

string    T_PV
[download]

(Safest to provide a fully qualified path to the typemap file - though a path relative to the cwd should also work.)

Cheers,
Rob