/*****************************************************************************/
// 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 <iomanip>
#include <sstream>
#include <iostream>

#include "statistics/Quality_Value_Stats.h"

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

Quality_Value_Stats::Quality_Value_Stats()
    : my_lane_num(0)
{
    ;
}

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

Quality_Value_Stats::~Quality_Value_Stats()
{
    ;
}

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

void Quality_Value_Stats::add_read_align_info(const Read_Align_Info&
                                              read_align_info)
{
    if (read_align_info.my_lane_num != my_lane_num) {
        if (my_lane_num == 0) {
            // First read.
            my_lane_num = read_align_info.my_lane_num;
        } else {
            std::cerr << "ERROR: Unexpected lane number "
                      << read_align_info.my_lane_num << " (expected " << my_lane_num << ")" << std::endl;
            throw std::range_error("");
        }
    }

    ++my_tile_num_freq_map[read_align_info.my_tile_num];

    my_all_quality_value_stats_set.add_read_align_info(read_align_info);

    if (read_align_info.passed_filter()) {
        my_passed_filter_quality_value_stats_set.
            add_read_align_info(read_align_info);
    }
}

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

bool Quality_Value_Stats::write_report(File_Buffer& file_buffer) const
{
    File_Buffer::Line_Vec line_vec;
    std::ostringstream ostrm;

    ostrm << " ** Quality value report **" << std::endl << std::endl
          << "Tiles analysed:" << std::endl;

    std::string separ_str("");

    for (Tile_Num_Freq_Map_CIter pair_citer(my_tile_num_freq_map.begin());
         pair_citer != my_tile_num_freq_map.end(); ++pair_citer) {
        ostrm << separ_str << "s_" << my_lane_num << "_"
              << std::setfill('0') << std::setw(4) << pair_citer->first;
        separ_str = " ";
    }

    ostrm << std::endl << my_tile_num_freq_map.size() << " tiles in all"
          << std::endl << std::endl
          << " ** Results for raw data **" << std::endl
          << my_all_quality_value_stats_set
          << std::endl << std::endl << std::endl
          << "Results for quality filtered data" << std::endl
          << my_passed_filter_quality_value_stats_set;

    line_vec.push_back(ostrm.str());

    if (!file_buffer.write_some_lines(line_vec)) {
        std::cerr << "ERROR: Failed to quality value statistics to "
                  << file_buffer.file_path_str() << std::endl;
        return false;
    }

    return true;
}

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