sequence_pac.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
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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>

namespace nvbio {
namespace io {

bool is_pac_archive(const char* sequence_file_name);

bool load_pac(
    const Alphabet              alphabet,
    SequenceDataHost*           sequence_data,
    const char*                 prefix,
    const SequenceFlags         load_flags,
    const QualityEncoding       qualities);

bool load_pac(
    const Alphabet                  alphabet,
    struct SequenceDataMMAPServer*  sequence_data,
    const char*                     prefix,
    const char*                     mapped_name,
    const SequenceFlags             load_flags,
    const QualityEncoding           qualities);


} // namespace io
} // namespace nvbio