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1 #define QF_LAMBDA 0.275
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2 #define QF_KARLIN 0.333
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3
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4
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5
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6 typedef struct {
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7 uint64_t id; //The thread id
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8 SeqInfo * database; //Database sequence and lengths
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9 SeqInfo * query; //Query sequence and lengths
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10 uint64_t from; //Starting READ to compute alignments from
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11 uint64_t to; //End READ to compute alignments from
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12 AVLContainer * container_a; //Container to hold the multidimensional array
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13 AVLContainer * container_b; //Container to hold the multidimensional array
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14 AVLContainer * container_c; //Container to hold the multidimensional array
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15 AVLContainer * container_d; //Container to hold the multidimensional array
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16 uint64_t * contained_reads;
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17 uint64_t * base_coordinates;
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18 uint64_t accepted_query_reads; //Number of reads that have a fragment with evalue less than specified
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19 long double min_e_value; //Minimum evalue to accept read
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20 long double min_coverage; //Minimum coverage percentage to accept read
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21 long double min_identity; //Minimum identity percentage to accept read
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22 long double window; //Percentage of window that will be explored (+-)
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23 FILE * out; //File to write alignments out
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24 int igap;
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25 int egap;
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26 uint64_t * hits; // To work in hits mode only
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27 struct positioned_cell * mc;
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28 struct cell ** table;
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29 char * reconstruct_X;
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30 char * reconstruct_Y;
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31 char * writing_buffer_alignment;
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32 unsigned char * my_x;
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33 unsigned char * my_y;
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34 Head * queue_head; //To tell where the queue starts after modifications
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35 pthread_mutex_t * lock;
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36 unsigned char full_comp; // Tells whether read reporting should stop at first match or keep reporting
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37 unsigned char * markers; // To tell which sequences were already used
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38 } HashTableArgs;
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39
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40
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41
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42 /*
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43 Nucleotides matching function
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44 */
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45 int64_t compare_letters(unsigned char a, unsigned char b);
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46
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47 /**
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48 * Initialize the memory pool to later retrieve individual memory addresses for llpos
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49 *
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50 */
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51 void init_mem_pool_llpos(Mempool_l * mp);
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52
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53 /**
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54 * Get a new memory address from the pool mp for a type llpos
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55 *
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56 */
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57 llpos * getNewLocationllpos(Mempool_l * mp, uint64_t * n_pools_used);
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58
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59 /*
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60 Load input database using 4 threads
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61 */
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62 void * load_input(void * a);
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63 /*
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64 Compute alignments by thread given a hash table argument
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65 */
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66 void * computeAlignmentsByThread(void * a);
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67
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68
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69 /*
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70 Performs NW and backtracking to recover alignment
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71 */
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72 void build_alignment(char * reconstruct_X, char * reconstruct_Y, uint64_t curr_db_seq, uint64_t curr_read, HashTableArgs * hta, unsigned char * my_x, unsigned char * my_y, struct cell ** table, struct positioned_cell * mc, char * writing_buffer_alignment, BasicAlignment * ba, uint64_t xlen, uint64_t ylen, int64_t * cell_path_y, long double * window);
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73
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74 /*
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75 Compute the alignment and evalue of a given hit
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76 The positions pos_database and pos_query refer to the last match in the hit
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77 */
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78 void alignmentFromQuickHits(SeqInfo * database, SeqInfo * query, uint64_t pos_database, uint64_t pos_query, uint64_t curr_read, uint64_t curr_db_seq, Quickfrag * qf, uint64_t offset_db_reads, uint64_t offset_db_coordinates);
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79
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80 /*
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81 Computes the cell path for the y points given incremental x
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82 Only add +- window size to each to know which path to go through
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83 */
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84 void calculate_y_cell_path(Point p0, Point p1, Point p2, Point p3, int64_t * cell_path_y);
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85 /*
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86 Calculates NW table with two rows and stores a cellpath of scores, identities, gaps and starting and ending positions
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87 */
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88 struct best_cell NW(unsigned char * X, uint64_t Xstart, uint64_t Xend, unsigned char * Y, uint64_t Ystart, uint64_t Yend, int64_t iGap, int64_t eGap, struct cell ** table, struct positioned_cell * mc, int show, int64_t * cell_path_y, long double * window, uint64_t * curr_window_size);
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89
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90 /*
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91 Computes the alignment given a NW table
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92 */
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93 void backtrackingNW(unsigned char * X, uint64_t Xstart, uint64_t Xend, unsigned char * Y, uint64_t Ystart, uint64_t Yend, struct cell ** table, char * rec_X, char * rec_Y, struct best_cell * bc, uint64_t * ret_head_x, uint64_t * ret_head_y, BasicAlignment * ba, int64_t * cell_path_y, uint64_t window_size);
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94
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95 /*
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96 Get memory for a new AVL tree node
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97 */
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98 AVLTree * getNewLocationAVLTree(Mempool_AVL * mp, uint64_t * n_pools_used, uint64_t key);
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99
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100 /*
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101 Initialize a memory pool for AVL trees
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102 */
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103 void init_mem_pool_AVL(Mempool_AVL * mp);
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104
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105 /*
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106 Right rotate an AVL tree to make it balanced
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107 */
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108 AVLTree * right_rotate(AVLTree * y);
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109
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110 /*
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111 Left rotate an AVL tree to make it balanced
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112 */
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113 AVLTree * left_rotate(AVLTree * x);
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114
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115
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116 /*
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117 Find a key in an AVL tree
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118 */
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119 AVLTree * find_AVLTree(AVLTree * node, uint64_t key);
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120
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121 /*
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122 Find a key in an AVL tree but return its hit list
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123 */
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124 llpos * find_AVLTree_llpos(AVLTree * node, uint64_t key);
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125
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126 /*
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127 Insert node in AVL tree
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128 */
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129 AVLTree * insert_AVLTree(AVLTree * node, uint64_t key, Mempool_AVL * mp, uint64_t * n_pools_used, uint64_t pos, Mempool_l * mp_l, uint64_t * n_pools_used_l, uint64_t s_id);
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130
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131 /*
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132 Traverse AVL tree in pre order
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133 */
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134 void pre_order(AVLTree * root);
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135
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136
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