diff options
Diffstat (limited to 'kmer_utils.c')
| -rw-r--r-- | kmer_utils.c | 16 |
1 files changed, 8 insertions, 8 deletions
diff --git a/kmer_utils.c b/kmer_utils.c index ce0aa81..51129ee 100644 --- a/kmer_utils.c +++ b/kmer_utils.c @@ -6,7 +6,7 @@ #include "kmer_total_count.h" -const unsigned char alpha[256] = +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, 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, @@ -26,13 +26,13 @@ const unsigned char alpha[256] = static const char reverse_alpha[4] = { 'A', 'C', 'G', 'T' }; -unsigned long long pow_four(unsigned long long x) { +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 num_to_index(const char *str, const int kmer, const long error_pos) { +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; @@ -54,7 +54,7 @@ unsigned long num_to_index(const char *str, const int kmer, const long error_pos } // convert an index back into a kmer string -char *index_to_kmer(unsigned long long index, long kmer) { +char *kmer_index_to_kmer(unsigned long long index, long kmer) { int i = 0; int j = 0; char *num_array = calloc(kmer, sizeof(char)); @@ -97,7 +97,7 @@ char *index_to_kmer(unsigned long long index, long kmer) { // Strip out any character 'c' from char array 's' into a destination dest (you // need to allocate that) and copy only len characters. -char *strnstrip(const char *s, char *dest, int c, unsigned long long len) { +static char *strnstrip(const char *s, char *dest, int c, unsigned long long len) { unsigned long long i = 0; unsigned long long j = 0; @@ -113,7 +113,7 @@ char *strnstrip(const char *s, char *dest, int c, unsigned long long len) { return dest; } -unsigned long long *get_kmer_counts_from_file(FILE *fh, const unsigned int kmer) { +unsigned long long *kmer_counts_from_file(FILE *fh, const unsigned int kmer) { char *line = NULL; size_t len = 0; ssize_t read; @@ -123,7 +123,7 @@ unsigned long long *get_kmer_counts_from_file(FILE *fh, const unsigned int kmer) // width is 4^kmer // there's a sneaky bitshift to avoid pow dependency - const unsigned long width = pow_four(kmer); + const unsigned long width = kmer_pow_four(kmer); // malloc our return array unsigned long long * counts = calloc((width+ 1), sizeof(unsigned long long)); @@ -170,7 +170,7 @@ unsigned long long *get_kmer_counts_from_file(FILE *fh, const unsigned int kmer) // 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]]; + str[i] = kmer_alpha[(int)str[i]]; } // loop through our string to process each k-mer |