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1 #include <stdio.h>
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2 #include <stdlib.h>
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3 #include <string.h>
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4 #include <ctype.h>
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5 #include "structs.h"
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6 #include "commonFunctions.h"
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7
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8 #define MAX(x, y) (((x) > (y)) ? (x) : (y))
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9 #define MIN(x, y) (((x) <= (y)) ? (x) : (y))
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10 #define STARTING_SEQS 1000
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11 #define PIECE_OF_DB_REALLOC 3200000 //half a gigabyte if divided by 8 bytes
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12 #define MATVAL 101
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13
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14 // void terror(char *s) {
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15 // fprintf(stdout, "ERR**** %s ****\n", s);
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16 // exit(-1);
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17 // }
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18
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19
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20 int main(int argc, char ** av){
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21
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22 if(argc != 2) terror("USE:: combine_reads <file>");
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23
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24
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25 char names[10][100] = {"14np", "47np", "BR0716C", "BR11044P", "CA01044C", "CA01067C", "CA11149P", "CA11154P", "MA07066C", "MA09032P"};
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26 uint64_t llen[10] = {1758451, 959020, 1616163, 884193, 934256, 1007436, 1670521, 584151, 671010, 516632};
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27 uint64_t nseqs = 10;
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28
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29 FILE * results, * data;
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30 data = fopen(av[1], "rt");
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31 if(data == NULL) terror("Could not open input file");
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32
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33 uint64_t * mat = (uint64_t *) calloc(MATVAL, sizeof(uint64_t));
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34 if(mat == NULL) terror("Could not allocate matrix array");
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35 long double * mat_e = (long double *) calloc(MATVAL, sizeof(long double));
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36 if(mat_e == NULL) terror("Could not allocate float table");
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37
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38 char current_file[100];
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39 uint64_t i=5, idx=0;
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40 while(av[1][i] != '_' && av[1][i+1] != 'g'){
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41 current_file[idx++] = av[1][i];
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42 i++;
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43 }
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44 current_file[idx] = '\0';
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45 fprintf(stdout, "Current file is %s\n", current_file);
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46
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47 char buffer[MAXLID];
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48 if ((results = fopen("accu.log", "r")) == NULL){
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49 results = fopen("accu.log", "wt");
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50 }else{
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51 // Load the matrix
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52
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53
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54 for(i=0;i<100;i++){
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55 if(0 == fgets(buffer, MAXLID, results)) terror("Missing number on load");
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56
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57 //fprintf(stdout, "Have %s\n", buffer);
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58 buffer[strlen(buffer)-1] = '\0';
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59 //mat[i] = asciiToUint64(buffer);
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60 mat_e[i] = (long double) atof(buffer);
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61 //fprintf(stdout, "%"PRIu64"\n", mat[i]);
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62 //getchar();
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63 }
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64 fclose(results);
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65 results = fopen("accu.log", "wt"); // Re open
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66 }
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67
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68 // Read file
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69 uint64_t read_id_1, read_id_2, coverage, identity, length, current, currmax, j, last = 100000, lastmax = 0xFFFFFFFFFFFFFFFF;
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70 while(!feof(data)){
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71 if(0 == fgets(buffer, MAXLID, data) && !feof(data)) terror("Missing values");
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72 // 2 77277 89 64 213
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73 sscanf(buffer, "%"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64, &read_id_1, &read_id_2, &coverage, &identity, &length);
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74 //fprintf(stdout, "%"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64"\n", read_id_1, read_id_2, coverage, identity, length);
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75 currmax = MIN(identity, coverage);
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76 //fprintf(stdout, "%"PRIu64"\n", currmax);
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77 current = read_id_1;
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78 /*
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79 for(j=currmax; j > 1; j--){
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80 if(current != lasts[j]){
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81 mat[j]++;
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82 lasts[j] = current;
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83 }
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84 }
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85 */
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86 if(lastmax == 0xFFFFFFFFFFFFFFFF){
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87 last = current;
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88 lastmax = 0;
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89 }
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90 if(current == last){
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91 //mat[currmax] += 1;
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92 if(lastmax < currmax){
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93 lastmax = currmax;
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94 }
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95 }else{
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96 mat[lastmax]++;
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97 last = current;
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98 lastmax = 0;
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99 }
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100
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101 }
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102
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103 uint64_t divider = 0;
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104 for(i=0; i < nseqs; i++){
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105
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106 if(strcmp(current_file, names[i]) == 0){
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107 divider = llen[i];
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108 }
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109 }
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110 if(divider == 0) terror("Could not find file for divider"); else fprintf(stdout, "The divider is %"PRIu64"\n", divider);
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111
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112 for(j=99; j>0; j--){
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113 mat[j] += mat[j+1];
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114 }
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115 mat[0] = mat[1];
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116
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117 for(j=0; j<100; j++){
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118 fprintf(stdout, "%"PRIu64" --> %.5f\n", mat[j], (float)((100*(long double)mat[j])/(long double)divider));
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119
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120 fprintf(results, "%.5f\n", (float)(mat_e[j] + ((100*(long double)mat[j])/(long double)divider))/2);
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121 }
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122
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123
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124 fclose(results);
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125 fclose(data);
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126 free(mat);
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127 return 0;
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128 }
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