output_batch.cpp

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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
 *      derived from this software without specific prior written permission.
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#include <nvbio/io/output/output_batch.h>
#include <nvbio/basic/timer.h>
#include <nvbio/basic/vector.h>

#include <stdio.h>
#include <stdarg.h>

namespace nvbio {
namespace io {

void HostOutputBatchSE::readback(const DeviceOutputBatchSE batch)
{
    count = batch.count;
    batch.readback_scores( alignments );
    batch.readback_cigars( cigar );
    batch.readback_mds( mds );
    batch.readback_mapq( mapq );
    batch.readback_ids( read_ids );
}

void HostOutputBatchPE::readback(const DeviceOutputBatchSE batch, const AlignmentMate mate)
{
    count = batch.count;
    batch.readback_scores( alignments[mate] );
    batch.readback_cigars( cigar[mate] );
    batch.readback_mds( mds[mate] );
    batch.readback_mapq( mapq[mate] );

    if (mate == MATE_1)
        batch.readback_ids( read_ids );
}

// copy scoring data to host, converting to io::AlignmentResult
void DeviceOutputBatchSE::readback_scores(thrust::host_vector<io::Alignment>& host_alignments) const
{
    // copy alignment data into a staging buffer
    host_alignments = alignments;
}

// copy CIGARs into host memory
void DeviceOutputBatchSE::readback_cigars(io::HostCigarArray& host_cigar) const
{
    host_cigar.array = cigar.array;
    nvbio::cuda::thrust_copy_vector(host_cigar.coords, cigar.coords);
}

// copy MD strings back to the host
void DeviceOutputBatchSE::readback_mds(nvbio::HostVectorArray<uint8>& host_mds) const
{
    host_mds = mds;
}

// copy mapq back to the host
void DeviceOutputBatchSE::readback_mapq(thrust::host_vector<uint8>& host_mapq) const
{
    host_mapq = mapq;
}

// copy mapq back to the host
void DeviceOutputBatchSE::readback_ids(thrust::host_vector<uint32>& host_ids) const
{
    if (read_ids)
        host_ids = *read_ids;
    else
        host_ids.resize(0);
}

} // namespace io
} // namespace nvbio