input_thread.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
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 *      names of its contributors may be used to endorse or promote products
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// input_thread.h
//

#pragma once

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

    InputStage(io::SequenceDataStream* file, const uint32 max_strings, const uint32 max_bps) :
        m_file          ( file ),
        m_max_strings   ( max_strings ),
        m_max_bps       ( max_bps )
    {}

    bool process(PipelineContext& context)
    {
        Timer timer;
        timer.start();

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

        log_debug(stderr, "    loading.. started (%u, %u)\n", m_max_strings, m_max_bps);
        const int ret = io::next( DNA, output, m_file, m_max_strings, m_max_bps );
        log_debug(stderr, "    loading.. done\n");

        timer.stop();
        m_time += timer.seconds();
        return ret;
    }

    io::SequenceDataStream*         m_file;
    uint32                          m_max_strings;
    uint32                          m_max_bps;
    float                           m_time;
};