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

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

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

__END__
__CPP__

static string do_SSW(const string query, const string ref) {
	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;
}