diff options
| -rw-r--r-- | kmer_utils.c | 39 |
1 files changed, 31 insertions, 8 deletions
diff --git a/kmer_utils.c b/kmer_utils.c index e21ddb9..8e793b6 100644 --- a/kmer_utils.c +++ b/kmer_utils.c @@ -136,9 +136,29 @@ static size_t calculate_mer(const char *str, size_t str_len, size_t *pos, size_t return mer; } +static size_t fread_save_n_bytes(char *buffer, FILE *fh, size_t save_size, size_t buffer_size, size_t len) { + + if(ftell(fh) == 0) { + fread(buffer, 1, buffer_size, fh); + len = buffer_size - save_size; + } + else { + + size_t read_size = buffer_size - save_size; + + memcpy(buffer, buffer + len, save_size); + + len = fread(buffer + save_size, 1, read_size, fh); + + } + + return len; +} + unsigned long long *kmer_counts_from_file(FILE *fh, const unsigned int kmer) { - char buffer[BUFSIZ]; + char buffer[BUFSIZ] = { 0 }; bool header = false; + bool started = false; size_t len = 0; size_t position; @@ -152,19 +172,22 @@ unsigned long long *kmer_counts_from_file(FILE *fh, const unsigned int kmer) { exit(EXIT_FAILURE); } - while((len = fread(&buffer, 1, 4096, fh)) != NULL) { - size_t i = 0; - - // returns header state, - header = translate_nucleotides_to_numbers(buffer, len, kmer_alpha, &header); - + while((len = fread_save_n_bytes(buffer, fh, kmer, BUFSIZ - 1, len)) != NULL) { + size_t i; + + char *ptr = buffer; + if(started) + ptr = buffer + kmer; + + header = translate_nucleotides_to_numbers(ptr, len, kmer_alpha, &header); for(i = 0; i < (len - kmer + 1); i++) { size_t mer = calculate_mer(buffer, len, &i, kmer, width); counts[mer]++; } - } + started = true; + } return counts; } |