fasta.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 <vector>
#include <stdio.h>
#include <stdlib.h>
#include <zlib/zlib.h>

namespace nvbio {




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

    ~FASTA_inc_reader();

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

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

    uint8 get();

private:
    gzFile m_file;

    std::vector<uint8> m_buffer;
    uint32             m_buffer_size;
    uint32             m_buffer_pos;
};

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

    ~FASTA_reader();

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

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

    uint8 get();

    void rewind();

private:
    gzFile m_file;

    std::vector<char>  m_id;
    std::vector<uint8> m_read;
    std::vector<uint8> m_buffer;
    uint32             m_buffer_size;
    uint32             m_buffer_pos;
};


} // namespace nvbio

#include <nvbio/fasta/fasta_inl.h>