diff options
| -rw-r--r-- | kmer_utils.c | 65 |
1 files changed, 18 insertions, 47 deletions
diff --git a/kmer_utils.c b/kmer_utils.c index 6c98b54..18e26a5 100644 --- a/kmer_utils.c +++ b/kmer_utils.c @@ -7,11 +7,13 @@ #include "kmer_total_count.h" -#define ERROR_CODE 5 -#define SPACE_CODE 6 +#define ERROR 5 +#define SPACE 6 const unsigned char kmer_alpha[256] = -{5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, + +// \n +{5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, // A C G @@ -34,36 +36,17 @@ unsigned long long kmer_pow_four(unsigned long long x) { return (unsigned long long)1 << (x * 2); } -// convert a string of k-mer size base-4 values into a -// base-10 index -unsigned long kmer_num_to_index(const char *str, const int kmer, const long error_pos) { - int i = 0; - unsigned long out = 0; - unsigned long multiply = 1; - - for(i = kmer - 1; i >= 0; i--){ - - if(str[i] >> 2) { - return error_pos; - } - - out += str[i] * multiply; - multiply = multiply << 2; - } - - return out; -} - // convert an index back into a kmer string char *kmer_index_to_kmer(unsigned long long index, long kmer) { + 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); - // this is the core of the conversion. modulus 4 for base 4 conversion while (index != 0) { num_array[i] = index % 4; @@ -96,24 +79,12 @@ char *kmer_index_to_kmer(unsigned long long index, long kmer) { return ret; } +// convert a string into values from a lookup array static void translate_nucleotides_to_numbers(char *str, size_t len, const unsigned char *lookup) { size_t i; - for(i = 0; i < len; ++i) { - if(isspace(str[i])) { - str[i] = SPACE_CODE; - } - else { - str[i] = lookup[(int)str[i]]; - } - } -} - -static int is_whitespace(char c) { - return c == SPACE_CODE; -} -static int is_error_char(char c) { - return c == ERROR_CODE; + for(i = 0; i < len; ++i) + 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) { @@ -122,21 +93,21 @@ static size_t calculate_mer(const char *str, size_t *pos, size_t kmer_len, size_ size_t i; // for each char in the k-mer check if it is an error char + multiply = (unsigned long long)1 << (kmer_len* 2); + multiply = multiply >> 2; for(i = *pos; i < *pos + kmer_len; ++i) { - if(is_whitespace(str[i])) { - continue; + if(str[i] == SPACE) { + continue; } - - if(is_error_char(str[i])) { - mer = error_mer; + if(str[i] == ERROR) { *pos = i; - return mer; + return error_mer; } // multiply this char in the mer by the multiply // and bitshift the multiply for the next round mer += str[i] * multiply; - multiply = multiply << 2; + multiply = multiply >> 2; } return mer; @@ -174,7 +145,7 @@ unsigned long long *kmer_counts_from_file(FILE *fh, const unsigned int kmer) { size_t seq_length = read - (seq - line); // relace A, C, G and T with 0, 1, 2, 3 respectively - // everything else is 5 + // unknowns are 5, newlines are 6 translate_nucleotides_to_numbers(seq, seq_length, kmer_alpha); // loop through our string to process each k-mer |