sequence_database.h

/*
 * Firepony
 *
 * Copyright (c) 2014-2015, NVIDIA CORPORATION
 * Copyright (c) 2015, Nuno Subtil <subtil@gmail.com>
 * 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 copyright holders 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 THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE
 * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
 * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include "types.h"
#include "string_database.h"
#include "segmented_database.h"

namespace firepony {

// sequence storage for a single chromosome
template <target_system system>
struct sequence_storage
{
    packed_vector<system, 4> bases;

    template <target_system other_system>
    void copy(const sequence_storage<other_system>& other)
    {
        bases.copy(other.bases);
    }

    void free(void)
    {
        bases.free();
    }
};

template <target_system system>
struct sequence_database_storage : public segmented_database_storage<system, sequence_storage>
{
    // shorthand for base type
    typedef segmented_database_storage<system, sequence_storage> base;
    using base::storage;

    // grab a reference to the sequence stream at a given coordinate
    LIFT_HOST_DEVICE
    typename packed_vector<system, 4>::const_stream_type get_sequence_data(uint16 id, uint32 offset) const
    {
        const auto& d = base::get_sequence(id);
        return d.bases.stream_at_index(offset);
    }
};

struct sequence_database_host : public sequence_database_storage<host>
{
    // host-only data
    string_database sequence_names;
};

// device storage is identical to the generic version
template <target_system system>
using sequence_database_device = sequence_database_storage<system>;

} // namespace firepony