// -*- 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 READ_ALIGN_INFO
#define READ_ALIGN_INFO

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

#include <string>

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

class Read_Align_Info {
public:
    Read_Align_Info();

    bool is_aligned() const { return my_aligned_flag; }
    bool passed_filter() const { return my_passed_filter_flag; }
    const std::string& raw_read_str() const { 
        return (my_num_deletions > 0) ? my_raw_read_str : my_read_str;
    }

    unsigned int my_lane_num;
    unsigned int my_tile_num;
    unsigned int my_read_num;
    bool my_passed_filter_flag;

    // without any padding to represent deletions
    // (only need to fill out if deletions are present).
    std::string my_raw_read_str;

    std::string my_read_str;
    std::string my_ref_str;
    std::string my_qual_str;

    unsigned char my_num_insertions;
    unsigned char my_num_deletions;

    bool my_aligned_flag;
    unsigned int my_align_score;

    static const char our_del_ch;
};

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

#endif // ! READ_ALIGN_INFO

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