#!/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, &alignment);
	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;
}