/**
 ** Copyright (c) 2007-2009 Illumina, Inc.
 **
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 **
 ** \file CalculateDiversityOptions.hh
 **
 ** \brief The accepted command line arguments for CalculateDiversity.
 **
 ** The accepted command line options for CalculateDiversity are -
 **
 **    max-fragment-size  -  To specify a maximum fragment size for the distribution.
 **    help, h            -  To print the usage message for the application
 **
 ** \author Stephen Allan
 **/
#ifndef CASAVAS_ALIGNMENT_CALCULATE_DIVERSITY_OPTIONS_HH
#define CASAVAS_ALIGNMENT_CALCULATE_DIVERSITY_OPTIONS_HH

#include <boost/filesystem.hpp>

#include "common/Program.hh"

namespace casava
{
namespace alignment
{

namespace fs = boost::filesystem;

class CalculateDiversityOptions : public casava::common::Options
{
public:
    unsigned int maximumFragmentSize;
    fs::path inputDirectory;
    fs::path outputFile;
    unsigned int processLane ;
    CalculateDiversityOptions();
    virtual ~CalculateDiversityOptions();
private:
    std::string usagePrefix()const {return "Usage: calculateDiversity [options]";}
};

} // namespace alignment
} // namespace casava

#endif // CASAVAS_ALIGNMENT_CALCULATE_DIVERSITY_OPTIONS_HH