/*****************************************************************************/
// 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).
/*****************************************************************************/

#include <sstream>
#include <iostream>
#include <getopt.h>

#include "statistics/PQVS_Options.h"

using namespace CommandLine;

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

PQVS_Options::PQVS_Options()
    : CommandLine::Options(),
      my_input_compr_name("none"),
      my_input_compr(File_Buffer::compressionNone)
{
    ;
}

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

PQVS_Options::~PQVS_Options()
{
    ;
}

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

int PQVS_Options::getOptions(int argc, char* const argv[])
    throw (CommandLine::UnknownOptionException,
           CommandLine::MissingOptionException,
           CommandLine::InvalidArgumentException)
{
    const char* short_option_cstr = "heaz:o:T:";

    const struct option long_option_arr[] =
        { {"help",                   no_argument, 0, 'h'},
          {"input_compr",      required_argument, 0, 'z'},
          {"output_file",       required_argument, 0, 'o'},
          {0, 0, 0, 0}
        };

    int long_option_index(0);
    int option(0);

        // Note: case 'h' returns immediately.
    while (-1 != (option = getopt_long(argc, argv,
                                       short_option_cstr, long_option_arr,
                                       &long_option_index))) {
        switch (option) {
        case 0:
            break;
        case 'h':
            return usage(argc, argv);
            break;
        case 'z':
            my_input_compr_name = optarg;
            break;
        case 'o':
            my_output_path_str = optarg;
            break;

        case '?':
        case ':':
        default:
            throw UnknownOptionException("");
            break;
        }
    }

    return RUN;
}

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

void PQVS_Options::processOptions()
    throw (CommandLine::InvalidArgumentException)
{
    std::string msg_str("input ");

    if (!resolve_compression(my_input_compr_name, my_input_compr, msg_str)) {
        throw InvalidArgumentException(msg_str);
    }
}

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

void PQVS_Options::getParameters(int argc, char* const argv[])
    throw (CommandLine::InvalidArgumentException)
{
    // Expecting exactly 1 export input file

    if (argc <= optind) {
        throw InvalidArgumentException("No input file specified.");
    }

    my_input_path_str = argv[optind++];
    const unsigned int num_unexpected_args(argc - optind);

    std::string msg_str("");

    switch (num_unexpected_args) {
    case 0:
        return;
    case 1:
        msg_str = "Unexpected argument `";
        break;
    default:
        msg_str = "Multiple unexpected arguments starting with `";
    }

    msg_str += (std::string(argv[optind]) + "'.");;
    throw InvalidArgumentException(msg_str);
}

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

int PQVS_Options::usage(int , char* const arg_cstr_arr[],
                        const std::string& msg_str)
{
    if (0 != msg_str.size()) {
        std::cerr << "ERROR: " << msg_str << std::endl;
    }

    const std::string app_name(arg_cstr_arr[0]);
    std::ostringstream ostrm;

    ostrm << "Usage : " << app_name << " -h|--help" << std::endl
          << "   OR : " << app_name << std::endl
          << "[-z|--input_compr <gzip|bzip2>]" << std::endl
          << "-o|--output_file <output_file>" << std::endl
          << "<input_file>" << std::endl;

    std::cerr << "INFO: " << ostrm.str() << std::endl;
    return NO_RUN;
}

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