//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// connect - Determine the complete sequence of a 
// paired end fragment by finding a walk that
// connects the ends.
//
#ifndef CONNECT_H
#define CONNECT_H
#include <getopt.h>
#include "config.h"
#include "BWT.h"
#include "Match.h"
#include "BWTAlgorithms.h"
#include "OverlapAlgorithm.h"

// functions

//
int connectMain(int argc, char** argv);

// options
void parseConnectOptions(int argc, char** argv);

#endif
