sequence_fasta.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:
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 *      notice, this list of conditions and the following disclaimer.
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 *      notice, this list of conditions and the following disclaimer in the
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 *      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/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 {




struct SequenceDataFile_FASTA_gz : public SequenceDataFile
{
    SequenceDataFile_FASTA_gz(
        const char*                         read_file_name,
        const SequenceDataFile::Options&    options);

    int nextChunk(SequenceDataEncoder *output, uint32 max_reads, uint32 max_bps);

    bool rewind();

private:
    FASTA_reader m_fasta_reader; 
};

struct SequenceDataOutputFile_FASTA : SequenceDataOutputStream
{
    SequenceDataOutputFile_FASTA(
        const char* file_name,
        const char* compressor,
        const char* options);

    void next(const SequenceDataHost& sequence_data);

    bool is_ok();

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


} // namespace io
} // namespace nvbio