Namespace all the functions and make private ones static

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];