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1 #ifndef STRUCTS_H
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2 #define STRUCTS_H
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3
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4 #include <inttypes.h>
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5
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6 //Structs required for the dotplot workflow
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7 #define MAXLID 200
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8 //#define READBUF 2000000000 //2 GB
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9 #define READBUF 500000000 //50MB
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10 #define INITSEQS 3000 //Number of starting sequences (in database)
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11 #define POINT 4
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12
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13 #define FIXED_K 12
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14 #define TOTAL_ENTRIES 16777216
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15
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16 #define MAXLID 200
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17 #define ALIGN_LEN 60 //For NW alignment
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18 #define MAX_READ_SIZE 20000 //Maximum length of read to have a portion of the table allocated
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19 #define MAX_WINDOW_SIZE 500 //Maximum window length to explore NW table
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20 //#define POOL_SIZE 2500000000 // by 16 bytes it is 40 GB
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21 #define POOL_SIZE 12500000 // 1 GB if 16 bytes
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22 #define MAX_MEM_POOLS 256
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23
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24 #define BYTES_IN_MER 4
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25 #define MAX_DECOMP_HASH 10
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26 #define FALSE 0
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27 #define TRUE 1
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28
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29 #define MAX(x, y) (((x) > (y)) ? (x) : (y))
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30 #define MIN(x, y) (((x) <= (y)) ? (x) : (y))
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31
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32 extern uint64_t custom_kmer;
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33 extern uint64_t diffuse_z;
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34
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35 //Struct for linked list of positions
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36 typedef struct linked_list_pos{
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37 uint64_t pos;
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38 //uint64_t extended_hash;
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39 //unsigned char decomp_hash[MAX_DECOMP_HASH]; // Fits up to MAX_DECOMP_HASH*4 letters = 256 length kmer
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40 //uint64_t hits_count;
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41 struct linked_list_pos * next;
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42 } llpos;
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43
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44
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45 // An AVL tree node
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46 typedef struct AVL_Node{
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47 uint64_t key;
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48 struct AVL_Node * left;
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49 struct AVL_Node * right;
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50 uint64_t height;
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51 uint64_t count;
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52 llpos * next;
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53 } AVLTree;
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54
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55
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56 // Tuple of data
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57 typedef struct tuple_hits{
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58 int repetition;
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59 int hit_count;
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60 uint64_t key;
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61 uint64_t pos;
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62 uint64_t pos_in_y;
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63 } Tuple_hits;
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64
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65 typedef struct hash_holder{
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66 uint64_t key;
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67 uint64_t pos;
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68 } Hash_holder;
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69
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70
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71
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72 //Struct for memory pool por lists
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73 typedef struct mempool_l{
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74 llpos * base;
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75 uint64_t current;
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76 } Mempool_l;
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77
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78 //Struct for memory pool por AVLtree
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79 typedef struct mempool_AVL{
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80 AVLTree * base;
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81 uint64_t current;
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82 } Mempool_AVL;
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83
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84 //Struct for a whole sequence(s) data
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85 typedef struct seqinfo{
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86 unsigned char * sequences;
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87 uint64_t * start_pos;
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88 uint64_t total_len;
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89 uint64_t n_seqs;
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90 } SeqInfo;
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91
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92 //Struct for the alignment of a quick hit
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93 typedef struct quickfrag{
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94 uint64_t x_start;
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95 uint64_t y_start;
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96 uint64_t t_len;
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97 long double coverage;
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98 long double e_value;
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99 } Quickfrag;
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100
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101 typedef struct point{
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102 uint64_t x;
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103 uint64_t y;
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104 } Point;
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105
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106
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107
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108 struct cell{
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109 int64_t score;
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110 uint64_t xfrom;
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111 uint64_t yfrom;
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112 };
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113
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114 struct positioned_cell{
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115 int64_t score;
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116 uint64_t xpos;
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117 uint64_t ypos;
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118 };
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119
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120 struct best_cell{
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121 struct positioned_cell c;
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122 uint64_t j_prime;
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123 };
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124
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125 typedef struct{
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126 uint64_t identities;
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127 uint64_t length;
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128 uint64_t igaps;
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129 uint64_t egaps;
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130 } BasicAlignment;
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131
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132 typedef struct queue{
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133 uint64_t r1; //reads region
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134 uint64_t r2;
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135 struct queue * next;
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136 } Queue;
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137
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138 typedef struct{
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139 Queue * head;
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140 } Head;
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141
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142
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143 #endif
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