xtn.h

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#include <vector>
const int MAX_COMPRESSED_LENGTH = 18;
int verboseGlobal = 0;
const char LEVENSHTEIN = 0;
const char HAMMING = 1;

struct Int3 {
    unsigned int entry[3] = {0, 0, 0};
    __device__ __host__
    bool operator==(const Int3& t) const {
        return (entry[0] == t.entry[0]) && (entry[1] == t.entry[1]) && (entry[2] == t.entry[2]);
    }
};

struct Int2 {
    int x = 0, y = 0;
    __device__ __host__
    bool operator==(const Int2& t) const {
        return (x == t.x) && (y == t.y);
    }
};

struct SeqInfo {
    int frequency, repertoire, originalIndex;
    __device__
    bool operator==(const SeqInfo& t) const;
};

struct XTNArgs {
    int distance = 1;
    int verbose = 0;
    char* seqPath = NULL;
    int seqLen = 0;
    char* outputPath = NULL;
    char measure = LEVENSHTEIN;
    char* infoPath = NULL;
    int infoLen = 0;
    int airr = 0;
};

struct MemoryContext {
    size_t gpuSize = 0;
    size_t ramSize = 0;
    int bandwidth1 = 0;
    int bandwidth2 = 0;
    int chunkSize = 0;
#ifdef TEST_ENV
    int histogramSize = 16;
    int maxThroughputExponent = 7;
#else
    int histogramSize = 65536;
    int maxThroughputExponent = 0;
#endif
};

struct XTNOutput {
    Int2* indexPairs = NULL;
    char* pairwiseDistances = NULL;
    size_t* pairwiseFrequencies = NULL;
    int len = 0;
};

enum ReturnCode {SUCCESS, ERROR, EXIT};

class SeqArray {
private:
    unsigned int *offsets, *offsets_d = NULL;
    std::vector<char> seqs;
    char* seqs_d = NULL;
    int size = 0;
    int maxSize = 0;

public:
    SeqArray(int seqLen);
    int append(char* inputStr);
    __device__
    int getItem(int index, char* &result);
    int getItemCPU(int index, char* &result);
    void toDevice();
    void destroy();
    int getSize();
    char* getSeqs_d();
    unsigned int* getOffsets_d();
};

void xtn_perform(XTNArgs args, SeqArray seqArr, SeqInfo* seqInfo, void callback (XTNOutput));