/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. 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 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
 * 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 NVIDIA CORPORATION 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 <nvbio/io/sequence/sequence.h>

/// initialize the MEM-search pipeline
///
void mem_init(struct pipeline_state *pipeline);

/// search MEMs for the given batch of reads
///
void mem_search(struct pipeline_state *pipeline, const nvbio::io::SequenceDataDevice *reads);

/// given the first read in a chunk, determine a suitably sized chunk of reads
/// (for which we can locate all MEMs in one go), updating pipeline::chunk
///
void fit_read_chunk(
    struct pipeline_state                   *pipeline,
    const nvbio::io::SequenceDataDevice     *batch,
    const nvbio::uint32                     read_begin);    // first read in the chunk

/// locate all mems in the range defined by pipeline::chunk
///
void mem_locate(struct pipeline_state *pipeline, const nvbio::io::SequenceDataDevice *reads);