/**
 ** 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.cpp
 **
 ** \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
 **/
#include "alignment/CalculateDiversityOptions.hh"

namespace casava
{
namespace alignment
{

CalculateDiversityOptions::CalculateDiversityOptions()
{
    namedOptions_.add_options()
        ("max-fragment-size", boost::program_options::value<unsigned int>(&maximumFragmentSize)->default_value(15000),
         "Maximum fragment size in the distribution.")
        ("input-directory", boost::program_options::value<fs::path>(&inputDirectory)->default_value("."),
         "Input directory.")
        ("output-file", boost::program_options::value<fs::path>(&outputFile)->default_value("./FragSizeDiversity_LW.txt"),
         "Full path to the output file.")
        ("lane", boost::program_options::value<unsigned int>(&processLane)->default_value(0),
         "Lane to be processed.")
        ;
}

CalculateDiversityOptions::~CalculateDiversityOptions()
{
}

}
}