Hi Rob, This indeed fixed the issue thank you very much! Here's the revised code:

#!/usr/bin/perl
use warnings;
use Inline CPP => Config => BUILD_NOISY => 1, CLEAN_AFTER_BUILD => 0,
    TYPEMAPS => './stringtype.map';
use Inline CPP;

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

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

__END__
__CPP__

using namespace std;
#include <string>
#include "ssw_cpp.h"
#include "ssw_cpp.cpp"
#include "ssw.c"
#include "ssw.h"

char *do_SSW(string queryC, string refC) {
    StripedSmithWaterman::Aligner aligner;
    StripedSmithWaterman::Filter filter;
    StripedSmithWaterman::Alignment alignment;
    aligner.Align(queryC.c_str(), refC.c_str(), refC.size(), filter, &
+alignment);
    string s     = alignment.cigar_string.c_str();
    char *a     = new char[s.size()+1];
    a[s.size()] = 0;
    memcpy(a,s.c_str(),s.size());
    return a;
}
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Having solved this problem, I am of course facing the next one: since the C++ alignment object contains more information and cannot be fully passed back to Perl right away, I am now trying to find a way to do so. My backup plan is to just concatenate all this information and then split the returned string in Perl.

Anyhow, again thanks a lot! René