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1 /*********
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2
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3 File CHROMEISTER.c
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4 Author EPW <estebanpw@uma.es>
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5 Description Computes hits and generates a dotplot
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6
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7 USAGE Usage is described by calling ./CHROMEISTER --help
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8
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9
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10
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11 **********/
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12
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13
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14 #include <stdio.h>
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15 #include <stdlib.h>
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16 #include <math.h>
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17 #include <string.h>
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18 #include <ctype.h>
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19 #include "structs.h"
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20 #include "alignmentFunctions.h"
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21 #include "commonFunctions.h"
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22 #define STARTING_SEQS 1000
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23 #define PIECE_OF_DB_REALLOC 3200000 //half a gigabyte if divided by 8 bytes
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24 #define RANGE 2
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25
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26 uint64_t custom_kmer = 32; // Defined as external in structs.h
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27 uint64_t diffuse_z = 4; // Defined as external in structs.h
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28
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29 uint64_t get_seq_len(FILE * f);
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30
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31
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32 void init_args(int argc, char ** av, FILE ** query, FILE ** database, FILE ** out_database, uint64_t * custom_kmer, uint64_t * dimension, uint64_t * diffuse_z);
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33
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34 int main(int argc, char ** av){
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35
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36
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37 /*
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38 //Store positions of kmers
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39 uint64_t n_pools_used = 0;
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40 //Mempool_l * mp = (Mempool_l *) malloc(MAX_MEM_POOLS*sizeof(Mempool_l));
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41 //if(mp == NULL) terror("Could not allocate vectors for memory pools");
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42 Mempool_l mp[MAX_MEM_POOLS];
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43 init_mem_pool_llpos(&mp[n_pools_used]);
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44 //llpos * aux;
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45
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46 uint64_t n_pools_used_AVL = 0;
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47 Mempool_AVL mp_AVL[MAX_MEM_POOLS];
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48 init_mem_pool_AVL(&mp_AVL[n_pools_used_AVL]);
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49 */
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50 Tuple_hits * thit;
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51
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52 /*
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53 AVLTree * root = NULL;
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54 root = insert_AVLTree(root, 10, mp_AVL, &n_pools_used_AVL, 0, mp, &n_pools_used);
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55
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56 llpos * some = find_AVLTree(root, 25);
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57 while(some != NULL){
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58 printf("#%"PRIu64", ", some->pos); some = some->next;
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59 }
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60 */
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61
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62 uint64_t i, j;
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63
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64 //query to read kmers from, database to find seeds
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65 FILE * query = NULL, * database = NULL, * out_database = NULL;
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66 uint64_t dimension = 1000; // Default 1000 * 1000
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67
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68
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69 init_args(argc, av, &query, &database, &out_database, &custom_kmer, &dimension, &diffuse_z);
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70
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71
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72
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73 unsigned char char_converter[91];
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74 char_converter[(unsigned char)'A'] = 0;
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75 char_converter[(unsigned char)'C'] = 1;
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76 char_converter[(unsigned char)'G'] = 2;
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77 char_converter[(unsigned char)'T'] = 3;
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78
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79
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80 // Variables to account for positions
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81 // Print info
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82 fprintf(stdout, "[INFO] Loading database\n");
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83 // Variables to read kmers
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84 char c = 'N'; //Char to read character
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85 // Current length of array and variables for the buffer
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86 uint64_t idx = 0, r = 0;
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87
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88 //Vector to read in batches
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89 char * temp_seq_buffer = NULL;
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90 if ((temp_seq_buffer = calloc(READBUF, sizeof(char))) == NULL) {
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91 terror("Could not allocate memory for read buffer");
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92 }
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93
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94 //Dimensional matrix
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95 uint64_t ** representation = (uint64_t **) calloc(dimension+1, sizeof(uint64_t *));
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96 if(representation == NULL) terror("Could not allocate representation");
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97 for(i=0; i<dimension+1; i++){
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98 representation[i] = (uint64_t *) calloc(dimension+1, sizeof(uint64_t));
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99 if(representation[i] == NULL) terror("Could not allocate second loop representation");
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100 }
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101
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102 /*
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103 fseek(database, 0, SEEK_END);
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104 uint64_t aprox_len_query = ftell(database);
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105 uint64_t aprox_len_db = aprox_len_query;
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106 rewind(database);
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107 */
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108 uint64_t aprox_len_query = get_seq_len(database);
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109 uint64_t aprox_len_db = aprox_len_query;
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110
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111 uint64_t a_hundreth = (aprox_len_query/100);
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112
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113 unsigned char curr_kmer[custom_kmer], reverse_kmer[custom_kmer];
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114 curr_kmer[0] = reverse_kmer[0] = '\0';
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115 uint64_t word_size = 0, word_size_rev = 0;
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116
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117 //To hold all information related to database
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118 uint64_t current_len = 0;
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119
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120 //To force reading from the buffer
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121 idx = READBUF + 1;
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122
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123 //unsigned char aux_kmer[custom_kmer+1];
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124
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125 //Vector to store query seq
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126 unsigned char * seq_vector_query = (unsigned char *) malloc(READBUF*sizeof(unsigned char));
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127 if(seq_vector_query == NULL) terror("Could not allocate memory for query vector");
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128
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129 /*
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130 Container * ct = (Container *) calloc(1, sizeof(Container));
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131 if(ct == NULL) terror("Could not allocate container");
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132 */
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133
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134
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135
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136 Index * ctidx = (Index *) calloc(1, sizeof(Index));
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137 if(ctidx == NULL) terror("Could not allocate container");
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138
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139
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140 //begin = clock();
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141
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142
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143 c = buffered_fgetc(temp_seq_buffer, &idx, &r, database);
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144 while((!feof(database) || (feof(database) && idx < r))){
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145
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146 if(c == '>'){
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147
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148
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149
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150 while(c != '\n') c = buffered_fgetc(temp_seq_buffer, &idx, &r, database); //Skip ID
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151
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152
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153 while(c != '>' && (!feof(database) || (feof(database) && idx < r))){ //Until next id
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154 c = buffered_fgetc(temp_seq_buffer, &idx, &r, database);
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155 c = toupper(c);
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156 if(c == 'A' || c == 'C' || c == 'G' || c == 'T'){
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157 curr_kmer[word_size] = (unsigned char) c;
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158 if(word_size < custom_kmer) ++word_size;
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159 ++current_len;
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160 if(current_len % a_hundreth == 0){
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161 fprintf(stdout, "\r%"PRIu64"%%...", 1+100*current_len/aprox_len_query);
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162 //printf("%"PRIu64"%%..wasted: (%e) (%e)", 1+100*pos_in_query/aprox_len_query, (double)(wasted_cycles_forward)/CLOCKS_PER_SEC, (double)(wasted_cycles_reverse)/CLOCKS_PER_SEC);
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163 fflush(stdout);
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164 }
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165
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166
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167
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168 }else{ //It can be anything (including N, Y, X ...)
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169
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170 if(c != '\n' && c != '>'){
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171 word_size = 0;
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172 // data_database.sequences[pos_in_database++] = (unsigned char) 'N'; //Convert to N
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173 ++current_len;
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174
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175 }
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176 }
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177 //if(current_len % 1000000 == 0) printf(" curr len %" PRIu64"\n", current_len);
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178 if(word_size == custom_kmer){
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179 //write to hash table
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180
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181
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182 thit = &ctidx->table[char_converter[curr_kmer[0]]][char_converter[curr_kmer[1]]][char_converter[curr_kmer[2]]]
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183 [char_converter[curr_kmer[3]]][char_converter[curr_kmer[4]]][char_converter[curr_kmer[5]]]
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184 [char_converter[curr_kmer[6]]][char_converter[curr_kmer[7]]][char_converter[curr_kmer[8]]]
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185 [char_converter[curr_kmer[9]]][char_converter[curr_kmer[10]]][char_converter[curr_kmer[11]]];
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186
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187 /*
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188 typedef struct tuple_hits{
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189 int repetition;
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190 int hit_count;
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191 uint64_t key;
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192 uint64_t pos;
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193 } Tuple_hits;
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194 */
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195
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196 if(thit->repetition == FALSE){
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197 // Then we can insert
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198 thit->hit_count = 0;
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199 thit->key = collisioned_hash(&curr_kmer[0], custom_kmer);
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200 thit->pos = current_len;
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201 }else{
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202 // Otherwise we break it
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203 thit->repetition = TRUE;
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204 }
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205
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206 //thit->root = insert_AVLTree(thit->root, hashOfWord(&curr_kmer[0], custom_kmer, FIXED_K), mp_AVL, &n_pools_used_AVL, current_len, mp, &n_pools_used);
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207 //thit->root = insert_AVLTree(thit->root, collisioned_hash(&curr_kmer[0], custom_kmer), mp_AVL, &n_pools_used_AVL, current_len, mp, &n_pools_used);
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208
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209
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210
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211 // Non overlapping
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212 word_size = 0;
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213
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214
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215 // Overlapping
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216 //memmove(&curr_kmer[0], &curr_kmer[1], custom_kmer-1);
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217 //--word_size;
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218 }
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219 }
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220 word_size = 0;
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221
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222 }else{
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223 c = buffered_fgetc(temp_seq_buffer, &idx, &r, database);
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224 }
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225
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226 }
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227
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228
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229 //end = clock();
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230
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231 // data_database.total_len = pos_in_database;
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232
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233 //fprintf(stdout, "[INFO] Database loaded and of length %"PRIu64". Hash table building took %e seconds\n", data_database.total_len, (double)(end-begin)/CLOCKS_PER_SEC);
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234 fprintf(stdout, "[INFO] Database loaded and of length %"PRIu64".\n", current_len);
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235 //close database
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236 fclose(database);
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237
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238
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239
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240 //begin = clock();
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241
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242
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243
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244
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245
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246 double pixel_size_db = (double) dimension / (double) current_len;
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247 double ratio_db = (double) current_len / dimension;
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248
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249
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250 // Get file length
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251
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252 //fseek(query, 0, SEEK_END);
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253 //aprox_len_query = ftell(query);
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254 //rewind(query);
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255 aprox_len_query = get_seq_len(query);
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256
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257 //uint64_t reallocs_hash_holder_table = 1;
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258 //uint64_t n_items_hash_holder_table = aprox_len_query / 5;
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259
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260 //Hash_holder * hash_holder_table = (Hash_holder *) calloc(n_items_hash_holder_table, sizeof(Hash_holder));
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261 //if(hash_holder_table == NULL) terror("Could not allocate hash holding table");
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262
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263 a_hundreth = (aprox_len_query/100);
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264 double pixel_size_query = (double) dimension / (double) aprox_len_query;
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265 double ratio_query = (double) aprox_len_query / dimension;
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266
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267
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268 double i_r_fix = MAX(1.0, custom_kmer * pixel_size_query);
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269 double j_r_fix = MAX(1.0, custom_kmer * pixel_size_db);
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270
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271
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272
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273 fprintf(stdout, "[INFO] Ratios: Q [%e] D [%e]. Lenghts: Q [%"PRIu64"] D [%"PRIu64"]\n", ratio_query, ratio_db, aprox_len_query, current_len);
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274 fprintf(stdout, "[INFO] Pixel size: Q [%e] D [%e].\n", pixel_size_query, pixel_size_db);
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275
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276
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277 fprintf(stdout, "[INFO] Computing absolute hit numbers.\n");
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278
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279
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280 current_len = 0;
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281
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282 //llpos * the_original_hit;
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283
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284 //To force reading from the buffer
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285 idx = READBUF + 1;
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286 c = buffered_fgetc(temp_seq_buffer, &idx, &r, query);
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287 //uint64_t c_hash_holder = 0;
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288
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289 while((!feof(query) || (feof(query) && idx < r))){
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290
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291 if(c == '>'){
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292 word_size = 0;
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293 word_size_rev = custom_kmer-1;
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294
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295
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296
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297
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298 while(c != '\n'){ c = buffered_fgetc(temp_seq_buffer, &idx, &r, query); } //Skip ID
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299
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300
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301 while(c != '>' && (!feof(query) || (feof(query) && idx < r))){ //Until next id
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302 c = buffered_fgetc(temp_seq_buffer, &idx, &r, query);
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303 c = toupper(c);
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304 if(c == 'A' || c == 'C' || c == 'G' || c == 'T'){
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305
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306 ++current_len;
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307 if(current_len % a_hundreth == 0){
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308 fprintf(stdout, "\r%"PRIu64"%%...", 1+100*current_len/aprox_len_query);
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309 fflush(stdout);
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310 }
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311 curr_kmer[word_size] = (unsigned char) c;
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312 ++word_size;
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313
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314 switch(c){
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315 case ('A'): reverse_kmer[word_size_rev] = (unsigned)'T';
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316 break;
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317 case ('C'): reverse_kmer[word_size_rev] = (unsigned)'G';
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318 break;
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319 case ('G'): reverse_kmer[word_size_rev] = (unsigned)'C';
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320 break;
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321 case ('T'): reverse_kmer[word_size_rev] = (unsigned)'A';
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322 break;
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323 }
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324 if(word_size_rev != 0) --word_size_rev;
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325
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326
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327
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328
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329 if(word_size == custom_kmer){
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330
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331
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332 //hash_forward = hashOfWord(&curr_kmer[0], custom_kmer, FIXED_K);
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333 //hash_reverse = hashOfWord(&reverse_kmer[0], custom_kmer, FIXED_K);
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334 uint64_t hash_forward, hash_reverse;
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335 hash_forward = collisioned_hash(&curr_kmer[0], custom_kmer);
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336 hash_reverse = collisioned_hash(&reverse_kmer[0], custom_kmer);
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337
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338
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339 thit = &ctidx->table[char_converter[curr_kmer[0]]][char_converter[curr_kmer[1]]][char_converter[curr_kmer[2]]]
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340 [char_converter[curr_kmer[3]]][char_converter[curr_kmer[4]]][char_converter[curr_kmer[5]]]
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341 [char_converter[curr_kmer[6]]][char_converter[curr_kmer[7]]][char_converter[curr_kmer[8]]]
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342 [char_converter[curr_kmer[9]]][char_converter[curr_kmer[10]]][char_converter[curr_kmer[11]]];
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343
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344 //AVLTree * search = find_AVLTree(thit->root, hash_forward);
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345
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346 if(thit->repetition == FALSE && hash_forward == thit->key){
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347 // Attention ::::: you were not removing the ones with count==1 earlier
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348 thit->pos_in_y = current_len;
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349 thit->hit_count++;
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350 }
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351
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352 thit = &ctidx->table[char_converter[reverse_kmer[0]]][char_converter[reverse_kmer[1]]][char_converter[reverse_kmer[2]]]
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353 [char_converter[reverse_kmer[3]]][char_converter[reverse_kmer[4]]][char_converter[reverse_kmer[5]]]
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354 [char_converter[reverse_kmer[6]]][char_converter[reverse_kmer[7]]][char_converter[reverse_kmer[8]]]
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355 [char_converter[reverse_kmer[9]]][char_converter[reverse_kmer[10]]][char_converter[reverse_kmer[11]]];
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356
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357 if(thit->repetition == FALSE && hash_reverse == thit->key){
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358 // Attention ::::: you were not removing the ones with count==1 earlier
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359 thit->pos_in_y = current_len;
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360 thit->hit_count++;
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361 }
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362
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363 /*
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364 if(search != NULL && search->count == 1){ //If count is two, then it is a rep
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365 thit->hit_count += search->count;
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366
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367 hash_holder_table[c_hash_holder].pos = current_len;
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368 hash_holder_table[c_hash_holder].node = search;
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369 hash_holder_table[c_hash_holder].th = thit;
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370 ++c_hash_holder;
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|
|
371 if(c_hash_holder == n_items_hash_holder_table*reallocs_hash_holder_table){
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|
|
372 ++reallocs_hash_holder_table;
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|
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373 hash_holder_table = (Hash_holder *) realloc(hash_holder_table, n_items_hash_holder_table*reallocs_hash_holder_table*sizeof(Hash_holder));
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|
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374 if(hash_holder_table == NULL) terror("Could not realloc hash holder table");
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375 }
|
|
|
376 }
|
|
|
377 */
|
|
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378
|
|
|
379
|
|
|
380
|
|
|
381
|
|
|
382
|
|
|
383 //search = find_AVLTree(thit->root, hash_reverse);
|
|
|
384 /*
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|
|
385 if(search != NULL && search->count == 1){ //If count is two, then it is a rep
|
|
|
386
|
|
|
387 thit->hit_count += search->count;
|
|
|
388 hash_holder_table[c_hash_holder].pos = current_len;
|
|
|
389 hash_holder_table[c_hash_holder].node = search;
|
|
|
390 hash_holder_table[c_hash_holder].th = thit;
|
|
|
391 ++c_hash_holder;
|
|
|
392 if(c_hash_holder == n_items_hash_holder_table*reallocs_hash_holder_table){
|
|
|
393 ++reallocs_hash_holder_table;
|
|
|
394 hash_holder_table = (Hash_holder *) realloc(hash_holder_table, n_items_hash_holder_table*reallocs_hash_holder_table*sizeof(Hash_holder));
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|
|
395 if(hash_holder_table == NULL) terror("Could not realloc hash holder table");
|
|
|
396 }
|
|
|
397 }
|
|
|
398 */
|
|
|
399
|
|
|
400 // Overlapping
|
|
|
401
|
|
|
402 memmove(&curr_kmer[0], &curr_kmer[1], custom_kmer-1);
|
|
|
403 memmove(&reverse_kmer[1], &reverse_kmer[0], custom_kmer-1);
|
|
|
404 --word_size;
|
|
|
405
|
|
|
406 // Non overlapping
|
|
|
407 //word_size = 0;
|
|
|
408 //word_size_rev = custom_kmer-1;
|
|
|
409 }
|
|
|
410 }else{
|
|
|
411 if(c != '\n' && c != '>'){
|
|
|
412 word_size = 0;
|
|
|
413 word_size_rev = custom_kmer-1;
|
|
|
414 ++current_len;
|
|
|
415 }
|
|
|
416 }
|
|
|
417 }
|
|
|
418 }else{
|
|
|
419 c = buffered_fgetc(temp_seq_buffer, &idx, &r, query);
|
|
|
420 }
|
|
|
421
|
|
|
422 }
|
|
|
423
|
|
|
424 /// Out
|
|
|
425
|
|
|
426 fprintf(stdout, "Scanning hits table.\n");
|
|
|
427
|
|
|
428 a_hundreth = MAX(1, TOTAL_ENTRIES/100);
|
|
|
429 uint64_t t_computed = 0;
|
|
|
430 uint64_t w0,w1,w2,w3,w4,w5,w6,w7,w8,w9,w10,w11;
|
|
|
431 for(w0=0;w0<4;w0++){
|
|
|
432 for(w1=0;w1<4;w1++){
|
|
|
433 for(w2=0;w2<4;w2++){
|
|
|
434 for(w3=0;w3<4;w3++){
|
|
|
435 for(w4=0;w4<4;w4++){
|
|
|
436 for(w5=0;w5<4;w5++){
|
|
|
437 for(w6=0;w6<4;w6++){
|
|
|
438 for(w7=0;w7<4;w7++){
|
|
|
439 for(w8=0;w8<4;w8++){
|
|
|
440 for(w9=0;w9<4;w9++){
|
|
|
441 for(w10=0;w10<4;w10++){
|
|
|
442 for(w11=0;w11<4;w11++){
|
|
|
443
|
|
|
444 if(t_computed % a_hundreth == 0){
|
|
|
445 fprintf(stdout, "\r%"PRIu64"%%...", 1+100*t_computed/TOTAL_ENTRIES);
|
|
|
446 fflush(stdout);
|
|
|
447 }
|
|
|
448 ++t_computed;
|
|
|
449 Tuple_hits * taux = &ctidx->table[w0][w1][w2][w3][w4][w5][w6][w7][w8][w9][w10][w11];
|
|
|
450 if(taux->hit_count == 1){
|
|
|
451 // We plot it
|
|
|
452 // Convert scale to representation
|
|
|
453 uint64_t redir_db = (uint64_t) (taux->pos / (ratio_db));
|
|
|
454 uint64_t redir_query = (uint64_t) (taux->pos_in_y / (ratio_query));
|
|
|
455 double i_r = i_r_fix; double j_r = j_r_fix;
|
|
|
456 while((uint64_t) i_r >= 1 && (uint64_t) j_r >= 1){
|
|
|
457 if((int64_t) redir_query - (int64_t) i_r > 0 && (int64_t) redir_db - (int64_t) j_r > 0){
|
|
|
458 representation[(int64_t) redir_query - (int64_t) i_r][(int64_t) redir_db - (int64_t) j_r]++;
|
|
|
459 }else{
|
|
|
460 representation[redir_query][redir_db]++;
|
|
|
461 break;
|
|
|
462 }
|
|
|
463 i_r -= MIN(1.0, pixel_size_query);
|
|
|
464 j_r -= MIN(1.0, pixel_size_db);
|
|
|
465 }
|
|
|
466 }
|
|
|
467 }
|
|
|
468 }
|
|
|
469 }
|
|
|
470 }
|
|
|
471 }
|
|
|
472 }
|
|
|
473 }
|
|
|
474 }
|
|
|
475 }
|
|
|
476 }
|
|
|
477 }
|
|
|
478 }
|
|
|
479
|
|
|
480
|
|
|
481 //double average_hit = ((double) total_hits / (double) table_size);
|
|
|
482 //average_hit = 2.2;
|
|
|
483
|
|
|
484 /*
|
|
|
485 //fprintf(stdout, "[INFO] Total hit count is %"PRIu64" on a size of %"PRIu64" Avg = %e.\n", total_hits, table_size, average_hit);
|
|
|
486 fprintf(stdout, "[INFO] Total hit count is %"PRIu64" on a size of %"PRIu64" E' = %e.\n", total_hits, table_size, Eprime);
|
|
|
487
|
|
|
488
|
|
|
489
|
|
|
490
|
|
|
491
|
|
|
492 a_hundreth = MAX(1,c_hash_holder/100);
|
|
|
493
|
|
|
494 for(current_len = 0; current_len < c_hash_holder; current_len++){
|
|
|
495
|
|
|
496 if(current_len % a_hundreth == 0){
|
|
|
497 fprintf(stdout, "\r%"PRIu64"%%...", 1+100*current_len/c_hash_holder);
|
|
|
498 fflush(stdout);
|
|
|
499 }
|
|
|
500
|
|
|
501 aux = hash_holder_table[current_len].node->next;
|
|
|
502
|
|
|
503 //if(hash_holder_table[current_len].th->hit_count < (uint64_t) average_hit){
|
|
|
504 if(hash_holder_table[current_len].th->hit_count < (uint64_t) Eprime){
|
|
|
505 while(aux != NULL){
|
|
|
506 // Convert scale to representation
|
|
|
507 uint64_t redir_db = (uint64_t) (aux->pos / (ratio_db));
|
|
|
508 uint64_t redir_query = (uint64_t) (hash_holder_table[current_len].pos / (ratio_query));
|
|
|
509 double i_r = i_r_fix; double j_r = j_r_fix;
|
|
|
510 while((uint64_t) i_r >= 1 && (uint64_t) j_r >= 1){
|
|
|
511 if((int64_t) redir_query - (int64_t) i_r > 0 && (int64_t) redir_db - (int64_t) j_r > 0){
|
|
|
512 representation[(int64_t) redir_query - (int64_t) i_r][(int64_t) redir_db - (int64_t) j_r]++;
|
|
|
513 }else{
|
|
|
514 representation[redir_query][redir_db]++;
|
|
|
515 break;
|
|
|
516 }
|
|
|
517 i_r -= MIN(1.0, pixel_size_query);
|
|
|
518 j_r -= MIN(1.0, pixel_size_db);
|
|
|
519 }
|
|
|
520 aux = aux->next;
|
|
|
521 }
|
|
|
522 }
|
|
|
523 }
|
|
|
524 */
|
|
|
525
|
|
|
526
|
|
|
527 //end = clock();
|
|
|
528
|
|
|
529
|
|
|
530
|
|
|
531
|
|
|
532 //fprintf(stdout, "\n[INFO] Query length %"PRIu64". Hits completed. Took %e seconds\n", data_query.total_len, (double)(end-begin)/CLOCKS_PER_SEC);
|
|
|
533 fprintf(stdout, "\n[INFO] Query length %"PRIu64".\n", current_len);
|
|
|
534
|
|
|
535 //begin = clock();
|
|
|
536
|
|
|
537 //reads_per_thread = (uint64_t) (floorl((long double) data_query.n_seqs / (long double) n_threads));
|
|
|
538
|
|
|
539 fprintf(stdout, "[INFO] Writing matrix.\n");
|
|
|
540
|
|
|
541
|
|
|
542 uint64_t unique_diffuse = 0;
|
|
|
543 fprintf(out_database, "%"PRIu64"\n", aprox_len_query);
|
|
|
544 fprintf(out_database, "%"PRIu64"\n", aprox_len_db);
|
|
|
545 // And replace 2's with 1's
|
|
|
546
|
|
|
547 for(i=0; i<dimension+1; i++){
|
|
|
548 for(j=0; j<dimension; j++){
|
|
|
549 fprintf(out_database, "%"PRIu64" ", representation[i][j]);
|
|
|
550 unique_diffuse += representation[i][j];
|
|
|
551 }
|
|
|
552 fprintf(out_database, "%"PRIu64"\n", representation[i][dimension]);
|
|
|
553 unique_diffuse += representation[i][dimension];
|
|
|
554 }
|
|
|
555
|
|
|
556 fprintf(stdout, "[INFO] Found %"PRIu64" unique hits for z = %"PRIu64".\n", unique_diffuse, diffuse_z);
|
|
|
557
|
|
|
558
|
|
|
559
|
|
|
560 //free(ct->table);
|
|
|
561 //free(hash_holder_table);
|
|
|
562 /*
|
|
|
563 for(i=0;i<=n_pools_used_AVL;i++){
|
|
|
564 free(mp_AVL[i].base);
|
|
|
565 }
|
|
|
566
|
|
|
567 for(i=0;i<=n_pools_used;i++){
|
|
|
568 free(mp[i].base);
|
|
|
569 }
|
|
|
570 */
|
|
|
571 for(i=0;i<dimension;i++){
|
|
|
572 free(representation[i]);
|
|
|
573 }
|
|
|
574 free(representation);
|
|
|
575 if(out_database != NULL) fclose(out_database);
|
|
|
576
|
|
|
577 return 0;
|
|
|
578 }
|
|
|
579
|
|
|
580 void init_args(int argc, char ** av, FILE ** query, FILE ** database, FILE ** out_database, uint64_t * custom_kmer, uint64_t * dimension, uint64_t * diffuse_z){
|
|
|
581
|
|
|
582 int pNum = 0;
|
|
|
583 while(pNum < argc){
|
|
|
584 if(strcmp(av[pNum], "--help") == 0){
|
|
|
585 fprintf(stdout, "USAGE:\n");
|
|
|
586 fprintf(stdout, " CHROMEISTER -query [query] -db [database] -out [outfile]\n");
|
|
|
587 fprintf(stdout, "OPTIONAL:\n");
|
|
|
588 fprintf(stdout, " -kmer [Integer: k>1 (default 32)]\n");
|
|
|
589 fprintf(stdout, " -diffuse [Integer: z>0 (default 4)]\n");
|
|
|
590 fprintf(stdout, " -dimension Size of the output [Integer: d>0 (default 1000)]\n");
|
|
|
591 fprintf(stdout, " -out [File path]\n");
|
|
|
592 fprintf(stdout, " --help Shows help for program usage\n");
|
|
|
593 fprintf(stdout, "\n");
|
|
|
594 fprintf(stdout, "PLEASE NOTICE: The reverse complementary is calculated for the QUERY.\n");
|
|
|
595 exit(1);
|
|
|
596 }
|
|
|
597 if(strcmp(av[pNum], "-query") == 0){
|
|
|
598 *query = fopen64(av[pNum+1], "rt");
|
|
|
599 if(query==NULL) terror("Could not open query file");
|
|
|
600 }
|
|
|
601 if(strcmp(av[pNum], "-db") == 0){
|
|
|
602 *database = fopen64(av[pNum+1], "rt");
|
|
|
603 if(database==NULL) terror("Could not open database file");
|
|
|
604 }
|
|
|
605 if(strcmp(av[pNum], "-out") == 0){
|
|
|
606 *out_database = fopen(av[pNum+1], "wt");
|
|
|
607 if(out_database==NULL) terror("Could not open output database file");
|
|
|
608 }
|
|
|
609 if(strcmp(av[pNum], "-kmer") == 0){
|
|
|
610 *custom_kmer = (uint64_t) atoi(av[pNum+1]);
|
|
|
611 if(*custom_kmer < BYTES_IN_MER) terror("K-mer size must be larger than 4");
|
|
|
612 if(*custom_kmer % BYTES_IN_MER != 0) terror("K-mer size must be a multiple of 4");
|
|
|
613
|
|
|
614 }
|
|
|
615 if(strcmp(av[pNum], "-diffuse") == 0){
|
|
|
616 *diffuse_z = (uint64_t) atoi(av[pNum+1]);
|
|
|
617 if(*diffuse_z == 0 || *diffuse_z > 32) terror("Z must satisfy 0<z<=32");
|
|
|
618
|
|
|
619 }
|
|
|
620
|
|
|
621 if(strcmp(av[pNum], "-dimension") == 0){
|
|
|
622 *dimension = (uint64_t) atoi(av[pNum+1]);
|
|
|
623 if(*dimension < 1) terror("Dimension must be a positive integer");
|
|
|
624 }
|
|
|
625
|
|
|
626 pNum++;
|
|
|
627 }
|
|
|
628
|
|
|
629 if(*query==NULL || *database==NULL || *out_database==NULL) terror("A query, database and output file is required");
|
|
|
630 }
|
|
|
631
|
|
|
632 uint64_t get_seq_len(FILE * f) {
|
|
|
633 char c = '\0';
|
|
|
634 uint64_t l = 0;
|
|
|
635
|
|
|
636 while(!feof(f)){
|
|
|
637 c = getc(f);
|
|
|
638
|
|
|
639 if(c == '>'){
|
|
|
640 while(c != '\n') c = getc(f);
|
|
|
641 }
|
|
|
642 c = toupper(c);
|
|
|
643 if(c >= 'A' && c <= 'Z'){
|
|
|
644 ++l;
|
|
|
645 }
|
|
|
646 }
|
|
|
647
|
|
|
648
|
|
|
649 rewind(f);
|
|
|
650 return l;
|
|
|
651 }
|
