/*
 * 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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 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include <nvbio/io/sequence/sequence.h>
#include <nvbio/io/sequence/sequence_priv.h>
#include <nvbio/io/output_stream.h>
#include <nvbio/fasta/fasta.h>
#include <nvbio/basic/console.h>

namespace nvbio {
namespace io {

///@addtogroup IO
///@{

///@addtogroup SequenceIO
///@{

///@addtogroup SequenceIODetail
///@{

///
/// loader for FASTA files, possibly gzipped
///
struct SequenceDataFile_FASTA_gz : public SequenceDataFile
{
    /// constructor
    ///
    SequenceDataFile_FASTA_gz(
        const char*                         read_file_name,
        const SequenceDataFile::Options&    options);

    /// get a chunk of reads
    ///
    int nextChunk(SequenceDataEncoder *output, uint32 max_reads, uint32 max_bps);

    /// rewind the file
    ///
    bool rewind();

private:
    FASTA_reader m_fasta_reader; ///< the FASTA file parser
};

/// SequenceDataFile from a FASTQ file
/// contains the code to parse FASTQ files and dump the results into a SequenceDataRAM object
/// file access is done via derived classes
///
struct SequenceDataOutputFile_FASTA : SequenceDataOutputStream
{
    /// constructor
    ///
    SequenceDataOutputFile_FASTA(
        const char* file_name,
        const char* compressor,
        const char* options);

    /// next batch
    ///
    void next(const SequenceDataHost& sequence_data);

    /// return whether the stream is ok
    ///
    bool is_ok();

private:
    // file name we're reading from
    const char*   m_file_name;
    OutputStream* m_file;
};

///@} // SequenceIODetail
///@} // SequenceIO
///@} // IO

} // namespace io
} // namespace nvbio
