output_types.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:
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 *      notice, this list of conditions and the following disclaimer.
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 *      names of its contributors may be used to endorse or promote products
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#pragma once

#include <nvbio/basic/types.h>
#include <nvbio/io/alignments.h>

#include <nvbio/io/sequence/sequence.h>
#include <nvbio/basic/vector_array.h>

#include <thrust/host_vector.h>
#include <thrust/device_vector.h>

#include <nvbio/io/output/output_utils.h>

namespace nvbio {
namespace io {

// this was used by mapq.h in bowtie2, but seems to no longer be used anywhere
//struct MapQInfo
//{
//    int32 best;
//    int32 second_best;
//};

struct BNT
{
    uint32          n_seqs;
    const char*     names;
    const uint32*   names_index;
    const uint32*   sequence_index;

    BNT(const io::ConstSequenceDataView& reference)
        : n_seqs( reference.size() ),
          names( reference.name_stream() ),
          names_index( reference.name_index() ),
          sequence_index( reference.sequence_index() )
    {}
};

typedef enum {
    SINGLE_END,
    PAIRED_END
} AlignmentType;

typedef enum {
    MATE_1 = 0,
    MATE_2 = 1,
} AlignmentMate;

typedef enum {
    BEST_SCORE,
    SECOND_BEST_SCORE,
} AlignmentScore;

struct DeviceCigarArray
{
    nvbio::DeviceVectorArray<io::Cigar>&       array;
    thrust::device_vector<uint2>&              coords;

    DeviceCigarArray(nvbio::DeviceVectorArray<io::Cigar>& array,
                     thrust::device_vector<uint2>&        coords)
        : array(array),
          coords(coords)
    {}
};

struct HostCigarArray
{
    nvbio::HostVectorArray<io::Cigar>   array;
    thrust::host_vector<uint2>          coords;
};

typedef nvbio::HostVectorArray<uint8> HostMdsArray;

} // namespace io
} // namespace nvbio