/*
 * 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
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 *    * 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.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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 */

#pragma once

#include <nvbio/io/sequence/sequence.h>

/// initialize the alignment pipeline
///
void align_init(struct pipeline_state *pipeline, const nvbio::io::SequenceDataDevice *batch);

/// perform banded alignment
///
/// \return     the number of remaining active reads to align
///
nvbio::uint32 align(
    struct pipeline_state               *pipeline,
    const nvbio::io::SequenceDataHost   *reads_host,
    const nvbio::io::SequenceDataDevice *reads_device);