diff options
| -rw-r--r-- | kmer_utils.c | 18 |
1 files changed, 11 insertions, 7 deletions
diff --git a/kmer_utils.c b/kmer_utils.c index 73cf819..fb191b1 100644 --- a/kmer_utils.c +++ b/kmer_utils.c @@ -33,7 +33,7 @@ const unsigned char kmer_alpha[256] = static const char reverse_alpha[4] = { 'A', 'C', 'G', 'T' }; unsigned long long kmer_pow_four(unsigned long long x) { - return (unsigned long long)1 << (x * 2); + return 1ULL << (x * 2); } // convert an index back into a kmer string @@ -87,20 +87,25 @@ static void translate_nucleotides_to_numbers(char *str, size_t len, const unsign str[i] = lookup[(int)str[i]]; } -static size_t calculate_mer(const char *str, size_t *pos, size_t kmer_len, size_t error_mer) { +static size_t calculate_mer(const char *str, size_t str_len, size_t *pos, size_t kmer_len, size_t error_mer) { size_t mer = 0; size_t multiply; size_t i; size_t end; // set our multiplier to be pow(4, mer) >> 2; - multiply = (unsigned long long)1 << (kmer_len* 2); - multiply = multiply >> 2; + multiply = kmer_pow_four(kmer_len) >> 2; - // for each char in the k-mer check if it is an error char end = *pos + kmer_len; + + // check if space or error, otherwise bump our multiplier and mer for(i = *pos; i < end; ++i) { if(str[i] == SPACE) { + // if our end has been expanded to the max string length + // or if it is the first loop return the error length + if(end == str_len || i == *pos) + return error_mer; + end++; continue; } @@ -114,7 +119,6 @@ static size_t calculate_mer(const char *str, size_t *pos, size_t kmer_len, size_ mer += str[i] * multiply; multiply = multiply >> 2; } - return mer; } @@ -155,7 +159,7 @@ unsigned long long *kmer_counts_from_file(FILE *fh, const unsigned int kmer) { // loop through our string to process each k-mer for(position = 0; position < (seq_length - kmer + 1); position++) { - size_t mer = calculate_mer(seq, &position, kmer, width); + size_t mer = calculate_mer(seq, seq_length, &position, kmer, width); counts[mer]++; } } |