1 files changed, 24 insertions, 10 deletions

diff --git a/kmer_total_count.c b/kmer_total_count.c
index 4fadf03..113c979 100644
--- a/kmer_total_count.c
+++ b/kmer_total_count.c
@@ -7,7 +7,19 @@
 
 #include "kmer_utils.h"
 
-long position = 0;
+unsigned long position = 0;
+
+const unsigned char 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,
+5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5,
+5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 0, 5, 1, 5, 5, 5, 2,
+5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 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, 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, 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};
 
 int main(int argc, char **argv) {
 
@@ -16,14 +28,12 @@ int main(int argc, char **argv) {
   ssize_t read;
   long i = 0;
 
-  unsigned long long *counts;
-
   if(argc != 3) {
     printf("Please supply a filename and a kmer\n");
     exit(EXIT_FAILURE);
   }
 
-  FILE *fh = fopen(argv[1], "r");
+  FILE * const fh = fopen(argv[1], "r");
   if(fh == NULL) {
     fprintf(stderr, "Error opening %s - %s\n", argv[1], strerror(errno));
     exit(EXIT_FAILURE);
@@ -33,16 +43,20 @@ int main(int argc, char **argv) {
   const unsigned int kmer = atoi(argv[2]);
 
   // width is 4^kmer 
-  const unsigned long width = (int)pow(4, kmer);
+  const unsigned long width = pow(4, kmer);
 
   // malloc our counts matrix
-  counts = malloc((width+ 1) * sizeof(unsigned long long));
+  unsigned long long * const counts = malloc((width+ 1) * sizeof(unsigned long long));
+
   if(counts == NULL) 
     exit(EXIT_FAILURE);
-
+	
   while ((read = getline(&line, &len, fh)) != -1) {
     if(line[0] != '>' && read > kmer) {
-      convert_kmer_to_num(line, read);
+
+  		for(i = 0; i < read; i++) {
+				line[i] = alpha[line[i]];
+			}
 
       for(position = 0; position < (read - kmer); position++) {
         counts[num_to_index(&line[position],kmer, width)]++;
@@ -50,8 +64,8 @@ int main(int argc, char **argv) {
     } 
   }
 
-  for(i = 0; i < (unsigned)width; i++)
-    printf("%llu\n", counts[i]);
+  for(i = 0; i < (unsigned)width; i=i+4)
+    printf("%llu\n%llu\n%llu\n%llu\n", counts[i], counts[i+1], counts[i+2], counts[i+3]);
 
 
   return EXIT_SUCCESS;