agv_navigation_ws/fast_gicp/thirdparty/nvbio/nvmem/mem-search.h

/*
 * 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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#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);