diff options
| -rw-r--r-- | kmer_utils.c | 43 |
1 files changed, 20 insertions, 23 deletions
diff --git a/kmer_utils.c b/kmer_utils.c index c3ed028..80b82a0 100644 --- a/kmer_utils.c +++ b/kmer_utils.c @@ -154,30 +154,24 @@ char *strnstrip(const char *s, char *dest, int c, unsigned long long len) { return dest; } -unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned int kmer) { +unsigned long long * get_kmer_counts_from_file(FILE *fh, const unsigned int kmer) { - char *line = NULL; - size_t len = 0; - ssize_t read; + char *line = NULL; + size_t len = 0; + ssize_t read; - size_t i = 0; - size_t position = 0; - - FILE * const fh = fopen(fn, "r"); - if(fh == NULL) { - fprintf(stderr, "Error opening %s - %s\n", fn, strerror(errno)); - exit(EXIT_FAILURE); - } + long long i = 0; + long long position = 0; // 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 = calloc((width+ 1), sizeof(unsigned long long)); - if(counts == NULL) { + unsigned long long * counts = calloc((width+ 1), sizeof(unsigned long long)); + if(counts == NULL) { fprintf(stderr, strerror(errno)); - exit(EXIT_FAILURE); + exit(EXIT_FAILURE); } char *str = malloc(4096); @@ -189,16 +183,19 @@ unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned in unsigned long long str_size = 4096; while ((read = getdelim(&line, &len, '>', fh)) != -1) { + size_t k; + char *start; + size_t start_len; // find our first \n, this should be the end of the header - char *start = strchr(line, '\n'); + start = strchr(line, '\n'); if(start == NULL) continue; // point to one past that. start = start + 1; - size_t start_len = strlen(start); + start_len = strlen(start); // if our current str buffer isn't big enough, realloc @@ -217,14 +214,14 @@ unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned in // relace A, C, G and T with 0, 1, 2, 3 respectively // everything else is 5 - for(i = 0; i < seq_length; i++) { - str[i] = alpha[(int)str[i]]; - } + for(k = 0; k < seq_length; k++) + str[k] = alpha[(int)str[k]]; + // loop through our string to process each k-mer - for(position = 0; position < (seq_length - kmer + 1); position++) { - unsigned long mer = 0; - unsigned long multiply = 1; + for(position = 0; position < (signed)(seq_length - kmer + 1); position++) { + unsigned long long mer = 0; + unsigned long long multiply = 1; // for each char in the k-mer check if it is an error char for(i = position + kmer - 1; i >= position; i--){ |