input_thread.h

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/*
 * 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.
 * 
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 */

// input_thread.h
//

#pragma once

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

using namespace nvbio;


struct InputStageData
{
    InputStageData(io::SequenceDataStream* file, const uint32 max_strings, const uint32 max_bps) :
        m_file          ( file ),
        m_max_strings   ( max_strings ),
        m_max_bps       ( max_bps ),
        m_reads         ( 0 ),
        m_bps           ( 0 ),
        m_time          ( 0.0f )
    {}

    Mutex                           m_mutex;
    io::SequenceDataStream*         m_file;
    uint32                          m_max_strings;
    uint32                          m_max_bps;
    uint64                          m_reads;
    uint64                          m_bps;
    float                           m_time;
};

struct InputStage
{
    typedef void                   argument_type;
    typedef io::SequenceDataHost   return_type;

    InputStage() : m_data(NULL) {}

    InputStage(InputStageData* data) : m_data(data) {}

    bool process(PipelineContext& context)
    {
        m_data->m_mutex.lock();

        Timer timer;
        timer.start();

        // fetch the output
        io::SequenceDataHost* h_read_data = context.output<io::SequenceDataHost>();

        const int ret = io::next( DNA_N, h_read_data, m_data->m_file, m_data->m_max_strings, m_data->m_max_bps );

        timer.stop();
        m_data->m_time  += timer.seconds();
        m_data->m_reads += h_read_data->size();
        m_data->m_bps   += h_read_data->bps();

        if (h_read_data->max_sequence_len() > MAX_READ_LENGTH)
        {
            log_error(stderr, "  maximum read length exceeded: %u > %u\n", h_read_data->max_sequence_len(), MAX_READ_LENGTH);
            return false;
        }

        log_verbose(stderr, "\r  loaded reads [%llu, %llu] (%.1fM / %.2fG bps, %.1fK reads/s, %.1fM bps/s)                ",
            m_data->m_reads,
            m_data->m_reads + h_read_data->size(),
            1.0e-6f * (h_read_data->bps()),
            1.0e-9f * (m_data->m_bps + h_read_data->bps()),
            m_data->m_time ? (1.0e-3f * (m_data->m_reads + h_read_data->size())) / m_data->m_time : 0.0f,
            m_data->m_time ? (1.0e-6f * (m_data->m_bps   + h_read_data->bps() )) / m_data->m_time : 0.0f );
        log_debug_cont(stderr, "\n");

        m_data->m_mutex.unlock();

        return ret;
    }

    InputStageData*  m_data;
};