error_correct.h

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/*
 * 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
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 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

// error_correct.h
//

#pragma once

#include "utils.h"
#include <nvbio/basic/pipeline_context.h>
#include <nvbio/basic/numbers.h>
#include <nvbio/basic/console.h>
#include <nvbio/basic/timer.h>
#include <nvbio/basic/primitives.h>
#include <nvbio/io/sequence/sequence.h>
#include <stdio.h>
#include <stdlib.h>

using namespace nvbio;


struct ErrorCorrectStage
{
    typedef io::SequenceDataHost   argument_type;
    typedef io::SequenceDataHost   return_type;

    ErrorCorrectStage() {}

    ErrorCorrectStage(
        const int       _device,
        const uint32    _k,
        const uint64    _trusted_filter_size,
        const uint32*   _trusted_filter_storage,
              uint64*   _stats_vec,
        const float     _max_correction,
        const char      _bad_quality,
        const char      _new_quality,
        SequenceStats*  _stats) :
        device( _device ),
        k( _k ),
        trusted_filter_size( _trusted_filter_size ),
        trusted_filter_storage( _trusted_filter_storage ),
        stats_vec(_stats_vec),
        max_correction( _max_correction ),
        bad_quality( _bad_quality ),
        new_quality( _new_quality ),
        stats( _stats )
    {}

    bool process(PipelineContext& context);

    int                 device;
    uint32              k;
    uint64              trusted_filter_size;
    const uint32*       trusted_filter_storage;
          uint64*       stats_vec;
    float               max_correction;
    char                bad_quality;
    char                new_quality;
    SequenceStats*      stats;

    for_each_enactor<host_tag>   host_for_each;
    for_each_enactor<device_tag> device_for_each;
};