Hi Rob,

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.

Best, René 
#!/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;
}

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In reply to Re^4: Including existing C or CPP library using Inline by bontus
in thread Including existing C or CPP library using Inline by bontus

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