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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 //500MB
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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
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15 #define MAXLID 200
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16 #define ALIGN_LEN 60 //For NW alignment
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17 #define MAX_READ_SIZE 10000 //Maximum length of read to have a portion of the table allocated
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18 #define MAX_WINDOW_SIZE 1000 //Maximum window length to explore NW table
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19 //#define POOL_SIZE 2500000000 // by 16 bytes it is 40 GB
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20 #define POOL_SIZE 12500000 // 1 GB if 16 bytes
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21 #define MAX_MEM_POOLS 128
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22 #define FIXED_LOADING_THREADS 4
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23
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24 #define FALSE 0
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25 #define TRUE 1
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26
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27 extern uint64_t custom_kmer;
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28
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29 typedef char _vector_char __attribute__ ((vector_size (32*sizeof(char))));
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30
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31 //Struct for linked list of positions
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32 typedef struct linked_list_pos{
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33 uint64_t pos;
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34 uint64_t s_id;
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35 //uint64_t extended_hash;
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36 struct linked_list_pos * next;
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37 } llpos;
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38
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39 typedef struct AVL_Node{
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40 uint64_t key;
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41 struct AVL_Node * left;
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42 struct AVL_Node * right;
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43 uint64_t height;
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44 uint64_t count;
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45 llpos * next;
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46 } AVLTree;
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47
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48 //Struct for memory pool por lists
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49 typedef struct mempool_l{
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50 llpos * base;
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51 uint64_t current;
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52 } Mempool_l;
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53
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54 //Struct for memory pool por AVLtree
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55 typedef struct mempool_AVL{
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56 AVLTree * base;
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57 uint64_t current;
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58 } Mempool_AVL;
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59
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60
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61 //Struct for a whole sequence(s) data
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62 typedef struct seqinfo{
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63 unsigned char * sequences;
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64 uint64_t * start_pos;
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65 uint64_t total_len;
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66 uint64_t n_seqs;
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67 } SeqInfo;
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68
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69 //Struct for the alignment of a quick hit
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70 typedef struct quickfrag{
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71 uint64_t x_start;
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72 uint64_t y_start;
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73 uint64_t t_len;
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74 long double coverage;
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75 long double e_value;
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76 } Quickfrag;
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77
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78 typedef struct point{
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79 uint64_t x;
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80 uint64_t y;
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81 } Point;
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82
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83 typedef struct container{
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84 llpos * table[4][4][4][4][4][4][4][4][4][4][4]; // One reduced; A,C,G,T tables in use
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85 } Container;
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86
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87 typedef struct AVLcontainer{
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88 AVLTree root[4][4][4][4][4][4][4][4][4][4][4];
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89 } AVLContainer;
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90
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91 typedef struct{
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92 char * temp_seq_buffer;
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93 SeqInfo * data_database;
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94 uint64_t t_len;
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95 uint64_t word_size;
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96 uint64_t read_from;
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97 uint64_t read_to;
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98 uint64_t contained_reads;
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99 uint64_t base_coordinates;
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100 uint64_t n_allocs;
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101 char thread_id;
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102 AVLContainer * ct;
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103 Mempool_l * mp;
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104 uint64_t n_pools_used;
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105 uint64_t n_pools_used_AVL;
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106 Mempool_AVL * mp_AVL;
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107 } LoadingDBArgs;
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108
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109 struct cell{
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110 int64_t score;
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111 uint64_t xfrom;
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112 uint64_t yfrom;
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113 };
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114
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115 struct positioned_cell{
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116 int64_t score;
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117 uint64_t xpos;
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118 uint64_t ypos;
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119 };
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120
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121 struct best_cell{
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122 struct positioned_cell c;
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123 uint64_t j_prime;
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124 };
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125
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126 typedef struct{
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127 uint64_t identities;
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128 uint64_t length;
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129 uint64_t igaps;
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130 uint64_t egaps;
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131 } BasicAlignment;
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132
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133 typedef struct queue{
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134 uint64_t r1; //reads region
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135 uint64_t r2;
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136 struct queue * next;
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137 } Queue;
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138
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139 typedef struct{
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140 Queue * head;
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141 } Head;
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142
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143
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144 #endif
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