#!/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;
}