diff options
| -rw-r--r-- | src/c/kmer_utils.c | 42 | ||||
| -rw-r--r-- | src/c/multifasta_to_otu.c | 14 |
2 files changed, 28 insertions, 28 deletions
diff --git a/src/c/kmer_utils.c b/src/c/kmer_utils.c index 4926788..aa341f3 100644 --- a/src/c/kmer_utils.c +++ b/src/c/kmer_utils.c @@ -22,22 +22,22 @@ const unsigned char alpha[256] = // base-10 index unsigned long num_to_index(const char *str, const int kmer, const long error_pos) { - int i = 0; - unsigned long out = 0; - unsigned long multiply = 1; + int i = 0; + unsigned long out = 0; + unsigned long multiply = 1; - for(i = kmer - 1; i >= 0; i--){ + for(i = kmer - 1; i >= 0; i--){ if(str[i] == 5) { // position += i; return error_pos; } - out += str[i] * multiply; - multiply = multiply << 2; - } + out += str[i] * multiply; + multiply = multiply << 2; + } - return out; + return out; } // Strip out any character 'c' from char array 's' into a destination dest (you @@ -61,30 +61,30 @@ char *strnstrip(const char *s, char *dest, int c, unsigned long long len) { unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned int kmer) { - - char *line = NULL; - size_t len = 0; - ssize_t read; - long long i = 0; + char *line = NULL; + size_t len = 0; + ssize_t read; + + long long i = 0; long long position = 0; - FILE * const fh = fopen(fn, "r"); - if(fh == NULL) { - fprintf(stderr, "Error opening %s - %s\n", fn, strerror(errno)); - exit(EXIT_FAILURE); - } + FILE * const fh = fopen(fn, "r"); + if(fh == NULL) { + fprintf(stderr, "Error opening %s - %s\n", fn, strerror(errno)); + exit(EXIT_FAILURE); + } // width is 4^kmer // there's a sneaky bitshift to avoid pow dependency const unsigned long width = pow_four(kmer); // malloc our return array - unsigned long long * counts = malloc((width+ 1) * sizeof(unsigned long long)); + unsigned long long * counts = malloc((width+ 1) * sizeof(unsigned long long)); memset(counts, 0, width * sizeof(unsigned long long)); - if(counts == NULL) { + if(counts == NULL) { fprintf(stderr, strerror(errno)); - exit(EXIT_FAILURE); + exit(EXIT_FAILURE); } char *str = malloc(4096); diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index e060fcf..b6b0182 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -327,29 +327,29 @@ int main(int argc, char **argv) { printf("sequences: %llu\n", sequences); } - unsigned long long *solutions = malloc(dir_count * sequences * sizeof(unsigned long long)); + unsigned long long *solutions = malloc(dir_count * sequences * sizeof(unsigned long long)); check_malloc(solutions, NULL); - long long *file_sequence_count = calloc(dir_count, sizeof(long long)); + long long *file_sequence_count = calloc(dir_count, sizeof(long long)); check_malloc(file_sequence_count, NULL); #ifdef OMP - omp_set_num_threads(jobs); + omp_set_num_threads(jobs); #endif - printf("Beginning to process samples\n"); + printf("Beginning to process samples\n"); #pragma omp parallel for shared(solutions, sensing_matrix_ptr, width, done, sequences) - for(size_t i = 0; i < dir_count; i++ ) { + for(size_t i = 0; i < dir_count; i++ ) { size_t x = 0; size_t y = 0; size_t z = 0; unsigned long long file_sequence_count = 0; - unsigned long long rare_value = 0; - unsigned long long rare_width = 0; + unsigned long long rare_value = 0; + unsigned long long rare_width = 0; double rare_percent = 1.0; |