fastq.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
 *    * Neither the name of the NVIDIA CORPORATION nor the
 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include <nvbio/basic/types.h>
#include <nvbio/basic/console.h>
#include <vector>
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>

namespace nvbio {

#define FASTQ_EOF 255u




struct FASTQ_gzfile
{
    FASTQ_gzfile(const uint32 buffer_size = 64536u);

    FASTQ_gzfile(const char* filename, const uint32 buffer_size = 64536u);

    ~FASTQ_gzfile();

    void open(const char* filename);

    bool valid() const;

    uint8 get();

    uint32 read(uint8* buffer, const uint32 n);

    struct Impl;

private:
    Impl*              m_impl;
    std::vector<uint8> m_buffer;
    uint32             m_buffer_size;
    uint32             m_buffer_pos;
};

struct FASTQ_file
{
    FASTQ_file(const uint32 buffer_size = 64536u);
        
    FASTQ_file(const char* filename, const uint32 buffer_size = 64536u);

    void open(const char* filename);

    ~FASTQ_file();

    bool valid() const { return m_file != NULL; }

    uint8 get();

private:
    FILE*              m_file;
    std::vector<uint8> m_buffer;
    uint32             m_buffer_size;
    uint32             m_buffer_pos;
};

template <typename FASTQ_stream>
struct FASTQ_reader
{
    FASTQ_reader(FASTQ_stream& stream);

    ~FASTQ_reader() {}

    template <typename Writer>
    uint32 read(const uint32 n_reads, Writer& writer);

    uint8 get() { return m_stream->get(); };

    void error_string(char* error);

private:
    FASTQ_stream* m_stream;

    std::vector<char>  m_name;
    std::vector<uint8> m_read_bp;
    std::vector<uint8> m_read_q;

    uint32             m_error;
    char               m_error_char;
    uint32             m_line;
};

struct FASTQ_buffer
{
    FASTQ_buffer(const uint32 buffer_size, const char* buffer) :
        m_buffer( buffer ),
        m_buffer_size( buffer_size ),
        m_buffer_pos( 0 ) {}

    uint8 get()
    {
        return (m_buffer_pos < m_buffer_size) ? m_buffer[ m_buffer_pos++ ] : FASTQ_EOF;
    };

    const char* m_buffer;
    uint32      m_buffer_size;
    uint32      m_buffer_pos;
};


} // namespace nvbio

#include <nvbio/fastq/fastq_inl.h>