// -*- 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 ALIGN_FILE_DATA_H
#define ALIGN_FILE_DATA_H

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

#include "statistics/Align_Data.h"
#include "common/File_Buffer.h"

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

class Align_File_Data : public Align_Data
{
 public:
    Align_File_Data(const std::string& data_file_name,
                    const File_Buffer::Compression_Type compression
                    = File_Buffer::compressionNone);
    virtual ~Align_File_Data();

    virtual bool get_next_read_align_info(Read_Align_Info& read_align_info,
                                          bool& at_eof);

    virtual char blank_base();

 private:
    enum { NOT_ALIGNED_NUM_FIELDS = 3, ALIGNED_NUM_FIELDS = 7 };
    enum { READ_SEQ_FIELD_IND = 0,
           ALIGN_SCORE_FIELD_IND = 1,
           NUM_ALIGNS_FIELD_IND = 2,
           STRAND_DIR_FIELD_IND = 4,
           REF_SEQ_FIELD_IND = 5 };
};

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

#endif // ! ALIGN_FILE_DATA_H

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