annotate chromeister/src/structs.h @ 0:4616cc3476d4 draft

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#ifndef STRUCTS_H
#define STRUCTS_H

#include <inttypes.h>

//Structs required for the dotplot workflow
#define MAXLID 200
//#define READBUF 2000000000 //2 GB
#define READBUF 500000000 //50MB
#define INITSEQS 3000 //Number of starting sequences (in database)
#define POINT 4

#define FIXED_K 12
#define TOTAL_ENTRIES 16777216

#define MAXLID 200
#define ALIGN_LEN 60 //For NW alignment
#define MAX_READ_SIZE 20000 //Maximum length of read to have a portion of the table allocated
#define MAX_WINDOW_SIZE 500 //Maximum window length to explore NW table
//#define POOL_SIZE 2500000000 // by 16 bytes it is 40 GB
#define POOL_SIZE 12500000 // 1 GB if 16 bytes
#define MAX_MEM_POOLS 256 

#define BYTES_IN_MER 4
#define MAX_DECOMP_HASH 10
#define FALSE 0
#define TRUE 1

#define MAX(x, y) (((x) > (y)) ? (x) : (y))
#define MIN(x, y) (((x) <= (y)) ? (x) : (y))

extern uint64_t custom_kmer;
extern uint64_t diffuse_z;

//Struct for linked list of positions
typedef struct linked_list_pos{
    uint64_t pos;
    //uint64_t extended_hash;
    //unsigned char decomp_hash[MAX_DECOMP_HASH]; // Fits up to MAX_DECOMP_HASH*4 letters = 256 length kmer
    //uint64_t hits_count;
    struct linked_list_pos * next;
} llpos;


// An AVL tree node
typedef struct AVL_Node{
    uint64_t key;
    struct AVL_Node * left;
    struct AVL_Node * right;
    uint64_t height;
    uint64_t count;
    llpos * next;
} AVLTree;


// Tuple of data 
typedef struct tuple_hits{
    int repetition;
    int hit_count;
    uint64_t key;
    uint64_t pos;
    uint64_t pos_in_y;
} Tuple_hits;

typedef struct hash_holder{
    uint64_t key;
    uint64_t pos;
} Hash_holder;



//Struct for memory pool por lists
typedef struct mempool_l{
    llpos * base;
    uint64_t current;
} Mempool_l;

//Struct for memory pool por AVLtree
typedef struct mempool_AVL{
    AVLTree * base;
    uint64_t current;
} Mempool_AVL;

//Struct for a whole sequence(s) data
typedef struct seqinfo{
    unsigned char * sequences;
    uint64_t * start_pos;
    uint64_t total_len;
    uint64_t n_seqs;
} SeqInfo;

//Struct for the alignment of a quick hit
typedef struct quickfrag{
    uint64_t x_start;
    uint64_t y_start;
    uint64_t t_len;
    long double coverage;
    long double e_value;
} Quickfrag;

typedef struct point{
    uint64_t x;
    uint64_t y;
} Point;



struct cell{
    int64_t score;
    uint64_t xfrom;
    uint64_t yfrom;
};

struct positioned_cell{
    int64_t score;
    uint64_t xpos;
    uint64_t ypos;
};

struct best_cell{
    struct positioned_cell c;
    uint64_t j_prime;
};

typedef struct{
    uint64_t identities;
    uint64_t length;
    uint64_t igaps;
    uint64_t egaps;
} BasicAlignment;

typedef struct queue{
    uint64_t r1; //reads region
    uint64_t r2;
    struct queue * next;
} Queue;

typedef struct{
    Queue * head;
} Head;


#endif