diff options
| -rw-r--r-- | kmer_utils.c | 25 |
1 files changed, 12 insertions, 13 deletions
diff --git a/kmer_utils.c b/kmer_utils.c index a2fed0e..3b38985 100644 --- a/kmer_utils.c +++ b/kmer_utils.c @@ -11,7 +11,7 @@ #define ERROR 5 #define SPACE 6 -#define BUFSIZ 256 +#define BUFFER_SIZE 256 const unsigned char kmer_alpha[256] = // \n @@ -159,12 +159,11 @@ static size_t fread_save_n_bytes(char *buffer, FILE *fh, size_t save_size, size_ } unsigned long long *kmer_counts_from_file(FILE *fh, const unsigned int kmer) { - char buffer[BUFSIZ] = { 0 }; + char buffer[BUFFER_SIZE] = { 0 }; bool header = false; bool started = false; size_t len = 0; - size_t position; const unsigned long width = kmer_pow_four(kmer); @@ -175,17 +174,17 @@ unsigned long long *kmer_counts_from_file(FILE *fh, const unsigned int kmer) { exit(EXIT_FAILURE); } - size_t save_size = kmer - 1; - while((len = fread_save_n_bytes(buffer, fh, save_size, BUFSIZ - 1, len)) != NULL) { + size_t save_size = kmer - 1; + while((len = fread_save_n_bytes(buffer, fh, save_size, BUFFER_SIZE - 1, len)) != 0) { size_t i; - char *ptr = buffer + save_size; - size_t ptr_len = len; - - if(!started) { - ptr_len = len + save_size; - ptr = buffer; - } - + char *ptr = buffer + save_size; + size_t ptr_len = len; + + if(!started) { + ptr_len = len + save_size; + ptr = buffer; + } + header = translate_nucleotides_to_numbers(ptr, ptr_len, kmer_alpha, header); for(i = 0; i < (len - kmer + 1); i++) { |