sequence_bam.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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 *      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 <zlib/zlib.h>

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

namespace nvbio {
namespace io {




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

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

    virtual bool rewind();

    bool init(void);

private:
    bool readData(void *output, unsigned int len);

    gzFile fp;              
};


} // namespace io
} // namespace nvbio