diff options
| -rw-r--r-- | src/c/quikr_functions.c | 83 |
1 files changed, 41 insertions, 42 deletions
diff --git a/src/c/quikr_functions.c b/src/c/quikr_functions.c index 89f0698..595d2dc 100644 --- a/src/c/quikr_functions.c +++ b/src/c/quikr_functions.c @@ -13,10 +13,10 @@ void check_malloc(void *ptr, char *error) { if (ptr == NULL) { if(error != NULL) { - fprintf(stderr,"Error: %s\n", error); - } + fprintf(stderr,"Error: %s\n", error); + } else { fprintf(stderr, "Error: Could not allocate enough memory - %s\n", strerror(errno)); - } + } exit(EXIT_FAILURE); } } @@ -46,42 +46,42 @@ void debug_arrays(double *count_matrix, struct matrix *sensing_matrix) { void normalize_matrix(double *matrix, unsigned long long height, unsigned long long width) { - unsigned long long x = 0; - unsigned long long y = 0; + unsigned long long x = 0; + unsigned long long y = 0; - for(x = 0; x < height; x++) { + for(x = 0; x < height; x++) { - double row_sum = 0; + double row_sum = 0; - for(y = 0; y < (width); y++) - row_sum = row_sum + matrix[width * x + y]; - for(y = 0; y < (width); y++) - matrix[width * x + y] = matrix[width * x + y] / row_sum; - } + for(y = 0; y < (width); y++) + row_sum = row_sum + matrix[width * x + y]; + for(y = 0; y < (width); y++) + matrix[width * x + y] = matrix[width * x + y] / row_sum; + } } -unsigned long long count_sequences(const char *filename) { - char *line = NULL; - size_t len = 0; - ssize_t read; +unsigned long long count_sequences(const char *filename) { + char *line = NULL; + size_t len = 0; + ssize_t read; - unsigned long long sequences = 0; + unsigned long long sequences = 0; - FILE *fh = fopen(filename, "r"); - if(fh == NULL) { - fprintf(stderr, "could not open \"%s\"\n", filename ); + FILE *fh = fopen(filename, "r"); + if(fh == NULL) { + fprintf(stderr, "could not open \"%s\"\n", filename ); return 0; - } + } - while ((read = getline(&line, &len, fh)) != -1) { - if(line[0] == '>') - sequences++; - } + while ((read = getline(&line, &len, fh)) != -1) { + if(line[0] == '>') + sequences++; + } - free(line); - fclose(fh); + free(line); + fclose(fh); - return sequences; + return sequences; } @@ -94,20 +94,20 @@ struct matrix *load_sensing_matrix(const char *filename, unsigned int target_kme unsigned int kmer = 0; - unsigned long long i = 0; + unsigned long long i = 0; unsigned long long *row = NULL; unsigned long long sequences = 0; unsigned long long width = 0; - struct matrix *ret = NULL; + struct matrix *ret = NULL; - gzFile fh = NULL; + gzFile fh = NULL; - fh = gzopen(filename, "r"); - if(fh == NULL) { - fprintf(stderr, "could not open %s", filename); - exit(EXIT_FAILURE); - } + fh = gzopen(filename, "r"); + if(fh == NULL) { + fprintf(stderr, "could not open %s", filename); + exit(EXIT_FAILURE); + } line = malloc(1024 * sizeof(char)); check_malloc(line, NULL); @@ -150,18 +150,18 @@ struct matrix *load_sensing_matrix(const char *filename, unsigned int target_kme width = pow_four(kmer); // allocate a +1 size for the extra row - matrix = malloc(sequences * (width) * sizeof(double)); + matrix = malloc(sequences * (width) * sizeof(double)); check_malloc(matrix, NULL); row = malloc((width) * sizeof(unsigned long long)); check_malloc(row, NULL); - headers = malloc(sequences * sizeof(char *)); + headers = malloc(sequences * sizeof(char *)); check_malloc(headers, NULL); for(i = 0; i < sequences; i++) { unsigned long long j = 0; - // get header and add it to headers array + // get header and add it to headers array char *header = malloc(256 * sizeof(char)); check_malloc(header, NULL); gzgets(fh, header, 256); @@ -189,17 +189,16 @@ struct matrix *load_sensing_matrix(const char *filename, unsigned int target_kme } } - for(j = 0; j < width; j++) { + for(j = 0; j < width; j++) { matrix[i*(width) + j] = ((double)row[j]); } } // load the matrix of counts - gzclose(fh); + gzclose(fh); free(line); free(row); - ret = malloc(sizeof(struct matrix)); (*ret).kmer = kmer; (*ret).sequences = sequences; |