diff options
| -rw-r--r-- | kmer_counts_per_sequence.c | 4 | ||||
| -rw-r--r-- | kmer_total_count.c | 8 | ||||
| -rw-r--r-- | kmer_utils.c | 16 | ||||
| -rw-r--r-- | kmer_utils.h | 13 |
4 files changed, 20 insertions, 21 deletions
diff --git a/kmer_counts_per_sequence.c b/kmer_counts_per_sequence.c index 6557d5d..6ff815d 100644 --- a/kmer_counts_per_sequence.c +++ b/kmer_counts_per_sequence.c @@ -46,11 +46,11 @@ int main(int argc, char **argv) { memset(counts, 0, width * sizeof(unsigned long long)); for(i = 0; i < read - kmer; i++) { - line[i] = alpha[(int)line[i]]; + line[i] = kmer_alpha[(int)line[i]]; } for(i = 0; i < read - kmer; i++) { - counts[num_to_index(&line[i],kmer, width)]++; + counts[kmer_num_to_index(&line[i],kmer, width)]++; } for(i = 0; i < width; i++) diff --git a/kmer_total_count.c b/kmer_total_count.c index 5dbb50d..2f944d8 100644 --- a/kmer_total_count.c +++ b/kmer_total_count.c @@ -80,9 +80,9 @@ int main(int argc, char **argv) { exit(EXIT_FAILURE); } - width = pow_four(kmer); + width = kmer_pow_four(kmer); - unsigned long long *counts = get_kmer_counts_from_file(fh, kmer); + unsigned long long *counts = kmer_counts_from_file(fh, kmer); // If nonzero is set, only print non zeros if(nonzero) { @@ -90,7 +90,7 @@ int main(int argc, char **argv) { if(label) { for(i = 0; i < width; i++) if(counts[i] != 0) { - char *kmer_str = index_to_kmer(i, kmer); + char *kmer_str = kmer_index_to_kmer(i, kmer); fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]); free(kmer_str); } @@ -106,7 +106,7 @@ int main(int argc, char **argv) { if(label) { for(i = 0; i < width; i++) { if(counts[i] != 0) { - char *kmer_str = index_to_kmer(i, kmer); + char *kmer_str = kmer_index_to_kmer(i, kmer); fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]); free(kmer_str); } 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 diff --git a/kmer_utils.h b/kmer_utils.h index 9f4d34f..5932316 100644 --- a/kmer_utils.h +++ b/kmer_utils.h @@ -1,11 +1,10 @@ // Kmer functions -void convert_kmer_to_num(char *str, unsigned long length); -unsigned long num_to_index(const char *str, const int kmer, long error_pos); -char *index_to_kmer(unsigned long long index, long kmer); -unsigned long long * get_kmer_counts_from_file(FILE *fh, int kmer); +void kmer_convert_kmer_to_num(char *str, unsigned long length); +unsigned long kmer_num_to_index(const char *str, const int kmer, long error_pos); +char *kmer_index_to_kmer(unsigned long long index, long kmer); +unsigned long long * kmer_counts_from_file(FILE *fh, int kmer); // Utility functions -char *strnstrip(const char *s, char *dest, int c, int len); -unsigned long long pow_four(unsigned long long x); +unsigned long long kmer_pow_four(unsigned long long x); -extern const unsigned char alpha[256]; +extern const unsigned char kmer_alpha[256]; 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