output_gzip.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
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 * 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.
 * 
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 */

#pragma once

#include <nvbio/io/output/output_types.h>
#include <nvbio/io/output/output_databuffer.h>

#include <zlib/zlib.h>
#include <stdio.h>

namespace nvbio {
namespace io {

struct GzipCompressor
{
    GzipCompressor();

    void start_block(DataBuffer& output);
    void compress(DataBuffer& output, DataBuffer& input);
    virtual void end_block(DataBuffer& output);

protected:
    // the zlib stream for this object
    z_stream stream;
    // gzip header for the stream
    gz_header_s gzh;
};

struct BGZFCompressor : public GzipCompressor
{
    struct bgzf_extra_data
    {
        uint8  SI1;     // gzip subfield identifier 1
        uint8  SI2;     // gzip subfield identifier 2
        uint16 SLEN;    // length of subfield data

        uint16 BSIZE;   // BAM total block size - 1
    } extra_data;

    BGZFCompressor();

    virtual void end_block(DataBuffer& output);
};

} // namespace io
} // namespace nvbio