diff options
| -rw-r--r-- | kmer_utils.c | 41 |
1 files changed, 27 insertions, 14 deletions
diff --git a/kmer_utils.c b/kmer_utils.c index 6736279..ef46842 100644 --- a/kmer_utils.c +++ b/kmer_utils.c @@ -51,30 +51,43 @@ inline unsigned long num_to_index(const char *str, const int kmer, const long er // convert an index back into a kmer string char *index_to_kmer(unsigned long long index, long kmer) { - int num_array[64]; - char *ret = calloc(64, sizeof(char)); + int i = 0; + int j = 0; + char *num_array = calloc(kmer, sizeof(char)); + char *ret = calloc(kmer + 1, sizeof(char)); if(ret == NULL) exit(EXIT_FAILURE); - int i = 0; - int j = 0; + // this is the core of the conversion. modulus 4 for base 4 conversion while (index != 0) { num_array[i] = index % 4; index /= 4; i++; } - ret[i] = '\0'; + // for our first few nmers, like AAAAA, the output would only be "A" instead + // of AAAAA so we prepend it + for(j = 0; j < (kmer - i); j++) + ret[j] = 'A'; + + // our offset for how many chars we prepended + int offset = j; + // save i so we can print it + int start = i ; + + // decrement i by 1 to reverse the last i++ i--; + j = 0; - for(j = 0; j < (kmer - i -1); j++) - ret[j] = 'A'; + // reverse the array, as j increases, decrease i + for(j = 0; j < start; j++, i--) + ret[j + offset] = reverse_alpha[num_array[i]]; - for(; i>=0; i--) { - ret[i+j] = reverse_alpha[num_array[i]]; - } + // set our last character to the null termination byte + ret[kmer + 1] = '\0'; + free(num_array); return ret; } @@ -104,7 +117,7 @@ unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned in ssize_t read; long long i = 0; - long long posistion = 0; + long long position = 0; FILE * const fh = fopen(fn, "r"); if(fh == NULL) { @@ -161,15 +174,15 @@ unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned in } // loop through our string to process each k-mer - for(posistion = 0; posistion < (seq_length - kmer + 1); posistion++) { + for(position = 0; position < (seq_length - kmer + 1); position++) { unsigned long mer = 0; unsigned long multiply = 1; // for each char in the k-mer check if it is an error char - for(i = posistion + kmer - 1; i >= posistion; i--){ + for(i = position + kmer - 1; i >= position; i--){ if(str[i] == 5) { mer = width; - posistion = i; + position = i; goto next; } |