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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 int main(int argc, char ** av){
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15
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16 if(argc != 2) terror("USE:: combine_reads <file>");
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17
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18 FILE * results, * data;
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19 data = fopen(av[1], "rt");
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20 if(data == NULL) terror("Could not open input file");
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21
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22 uint64_t * mat = (uint64_t *) calloc(MATVAL, sizeof(uint64_t));
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23 if(mat == NULL) terror("Could not allocate matrix array");
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24
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25 char buffer[MAXLID];
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26 if ((results = fopen("accu.log", "r")) == NULL){
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27 results = fopen("accu.log", "wt");
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28 }else{
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29 // Load the matrix
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30 uint64_t i;
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31
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32 for(i=0;i<100;i++){
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33 if(0 == fgets(buffer, MAXLID, results)) terror("Missing number on load");
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34
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35 //fprintf(stdout, "Have %s\n", buffer);
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36 buffer[strlen(buffer)-1] = '\0';
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37 mat[i] = asciiToUint64(buffer);
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38 //fprintf(stdout, "%"PRIu64"\n", mat[i]);
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39 //getchar();
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40 }
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41 fclose(results);
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42 results = fopen("accu.log", "wt"); // Re open
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43 }
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44
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45 // Read file
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46 uint64_t read_id_1, read_id_2, coverage, identity, length, current, currmax, j;
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47 while(!feof(data)){
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48 if(0 == fgets(buffer, MAXLID, data) && !feof(data)) terror("Missing values");
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49 // 2 77277 89 64 213
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50 sscanf(buffer, "%"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64, &read_id_1, &read_id_2, &coverage, &identity, &length);
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51 //fprintf(stdout, "%"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64"\n", read_id_1, read_id_2, coverage, identity, length);
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52 currmax = MIN(identity, coverage);
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53 //fprintf(stdout, "%"PRIu64"\n", currmax);
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54 current = read_id_1;
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55 /*
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56 for(j=currmax; j > 1; j--){
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57 if(current != lasts[j]){
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58 mat[j]++;
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59 lasts[j] = current;
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60 }
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61 }
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62 */
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63 mat[currmax] += 1;
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64
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65 }
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66
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67 for(j=99; j>0; j--){
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68 mat[j] += mat[j+1];
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69 }
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70 mat[0] = mat[1];
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71
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72 for(j=0; j<100; j++){
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73 fprintf(stdout, "%"PRIu64"\n", mat[j]);
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74 fprintf(results, "%"PRIu64"\n", mat[j]);
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75 }
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76
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77
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78 fclose(results);
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79 fclose(data);
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80 free(mat);
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81 return 0;
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82 } |
