Mercurial > repos > alvarofaure > bitlab
diff chromeister/src/combine_reads.c @ 0:7fdf47a0bae8 draft
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author | alvarofaure |
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date | Wed, 12 Dec 2018 07:18:40 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chromeister/src/combine_reads.c Wed Dec 12 07:18:40 2018 -0500 @@ -0,0 +1,82 @@ +#include <stdio.h> +#include <stdlib.h> +#include <string.h> +#include <ctype.h> +#include "structs.h" +#include "commonFunctions.h" + +#define MAX(x, y) (((x) > (y)) ? (x) : (y)) +#define MIN(x, y) (((x) <= (y)) ? (x) : (y)) +#define STARTING_SEQS 1000 +#define PIECE_OF_DB_REALLOC 3200000 //half a gigabyte if divided by 8 bytes +#define MATVAL 101 + +int main(int argc, char ** av){ + + if(argc != 2) terror("USE:: combine_reads <file>"); + + FILE * results, * data; + data = fopen(av[1], "rt"); + if(data == NULL) terror("Could not open input file"); + + uint64_t * mat = (uint64_t *) calloc(MATVAL, sizeof(uint64_t)); + if(mat == NULL) terror("Could not allocate matrix array"); + + char buffer[MAXLID]; + if ((results = fopen("accu.log", "r")) == NULL){ + results = fopen("accu.log", "wt"); + }else{ + // Load the matrix + uint64_t i; + + for(i=0;i<100;i++){ + if(0 == fgets(buffer, MAXLID, results)) terror("Missing number on load"); + + //fprintf(stdout, "Have %s\n", buffer); + buffer[strlen(buffer)-1] = '\0'; + mat[i] = asciiToUint64(buffer); + //fprintf(stdout, "%"PRIu64"\n", mat[i]); + //getchar(); + } + fclose(results); + results = fopen("accu.log", "wt"); // Re open + } + + // Read file + uint64_t read_id_1, read_id_2, coverage, identity, length, current, currmax, j; + while(!feof(data)){ + if(0 == fgets(buffer, MAXLID, data) && !feof(data)) terror("Missing values"); + // 2 77277 89 64 213 + sscanf(buffer, "%"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64, &read_id_1, &read_id_2, &coverage, &identity, &length); + //fprintf(stdout, "%"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64" %"PRIu64"\n", read_id_1, read_id_2, coverage, identity, length); + currmax = MIN(identity, coverage); + //fprintf(stdout, "%"PRIu64"\n", currmax); + current = read_id_1; + /* + for(j=currmax; j > 1; j--){ + if(current != lasts[j]){ + mat[j]++; + lasts[j] = current; + } + } + */ + mat[currmax] += 1; + + } + + for(j=99; j>0; j--){ + mat[j] += mat[j+1]; + } + mat[0] = mat[1]; + + for(j=0; j<100; j++){ + fprintf(stdout, "%"PRIu64"\n", mat[j]); + fprintf(results, "%"PRIu64"\n", mat[j]); + } + + + fclose(results); + fclose(data); + free(mat); + return 0; +} \ No newline at end of file