Dear Monks,

My current task involves string alignments, for which I found a very promising C/C++ library that I would like to call from my Perl code. The library can be found here: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library

and an example for C++ usage can be found here:

https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/blob/master/src/example.cpp

What I had in mind is, to create either a subroutine or a separate module that passes the sequences (query and ref in the example) to the C function. Several variables can then store the returned results. Unfortunately, I do not even get the first part running with only one variable being returned (disclaimer: I am not a C programmer and Inline sounds cool, but is also new to me).

Based on the C++ package, I wrote the following piece to get a general understanding of what is going on, which results in "Undefined subroutine &main::do_SSW called at ./somePerl.pl line 8.". FYI, the CIGAR string is a compact format to display alignments, see:

http://genome.sph.umich.edu/wiki/SAM#What_is_a_CIGAR.3F

Many thanks in advance, any help is greatly appreciated. 
#!/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, &ali
+gnment);
    return alignment.cigar_string;
}

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In reply to Including existing C or CPP library using Inline by bontus

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