// -*- c++ -*-
/*****************************************************************************/
// Copyright (c) Illumina 2008
// Author: Richard Shaw
//
// 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).
/*****************************************************************************/

#ifndef PAS_OPTIONS_H
#define PAS_OPTIONS_H

/*****************************************************************************/

#include <string>
#include <list>

#include "statistics/Align_Data_Factory.h"
#include "common/CommandLine.hh"
#include "common/File_Buffer.h"

/*****************************************************************************/

namespace CommandLine = casava::common;

class PAS_Options : public CommandLine::Options
{
 public:
    PAS_Options();
    ~PAS_Options();

    std::string my_input_compr_name;
    File_Buffer::Compression_Type my_input_compr;

    typedef std::list<std::string> Path_Str_List;
    typedef Path_Str_List::const_iterator Path_Str_List_CIter;
    Path_Str_List my_input_path_str_list;
    std::vector<unsigned int> my_read_list;
    std::string my_output_dir_str;
    std::string my_output_qualifier_str;
    std::string my_tile_list_file_path_str;
    std::string my_stats_file_prefix;
    std::string my_sample_name;
    std::string my_barcode;
    size_t max_patterns_to_store;
 private:
    void add_read(const std::string &read);
    virtual int getOptions(int argc, char* const argv[])
        throw (CommandLine::UnknownOptionException,
               CommandLine::MissingOptionException,
               CommandLine::InvalidArgumentException);
    virtual void processOptions()
        throw (CommandLine::InvalidArgumentException);
    virtual void getParameters(int argc, char* const argv[])
        throw (CommandLine::InvalidArgumentException);
    virtual int usage(int argc, char* const argv[],
                      const std::string& message = "");
};

/*****************************************************************************/

#endif // ! PAS_OPTIONS_H

/*****************************************************************************/