From 12fd24e056d18e9f7ee8e1e47a42e47c843c98ff Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Wed, 11 Sep 2013 09:43:33 -0400
Subject: move declarations to top, make sure to use the appropriate type

---
 kmer_frequency_per_sequence.c |  5 +++--
 kmer_total_count.c            | 18 ++++++++++++------
 2 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/kmer_frequency_per_sequence.c b/kmer_frequency_per_sequence.c
index e876d57..7171193 100644
--- a/kmer_frequency_per_sequence.c
+++ b/kmer_frequency_per_sequence.c
@@ -14,9 +14,10 @@ int main(int argc, char **argv) {
   long kmer = 6;
   size_t len = 0;
   ssize_t read;
+  unsigned long width = 0;
 
   if(argc != 3) {
-    printf("Please supply a filename, and only a filename\n");
+    printf("Please supply a filename and a kmer\n");
     exit(EXIT_FAILURE);
   }
 
@@ -26,8 +27,8 @@ int main(int argc, char **argv) {
     exit(EXIT_FAILURE);
   }
 
+  width = (int)pow(4, kmer);
 
-  int width = (int)pow(4, kmer);
   while ((read = getline(&line, &len, fh)) != -1) {
     if(line[0] != '>')   {
 
diff --git a/kmer_total_count.c b/kmer_total_count.c
index 9e92976..3679025 100644
--- a/kmer_total_count.c
+++ b/kmer_total_count.c
@@ -14,9 +14,12 @@ int main(int argc, char **argv) {
   size_t len = 0;
   ssize_t read;
   unsigned int i = 0;
+  unsigned int kmer = 0;
+  unsigned int width = 0;
+  unsigned long long *counts;
 
   if(argc != 3) {
-    printf("Please supply a filename, and only a filename\n");
+    printf("Please supply a filename and a kmer\n");
     exit(EXIT_FAILURE);
   }
 
@@ -25,17 +28,20 @@ int main(int argc, char **argv) {
     fprintf(stderr, "Couldn't open: %s\n", argv[1]);
     exit(EXIT_FAILURE);
   }
-  
-  int kmer = atoi(argv[2]);
-  int width = (int)pow(4, kmer);
 
-  unsigned long long *counts = malloc((width+ 1) * sizeof(unsigned long long));
+  // second argument is the kmer
+  kmer = atoi(argv[2]);
+
+  // width is 4^kmer 
+  width = (int)pow(4, kmer);
+
+  // malloc our counts matrix
+  counts = malloc((width+ 1) * sizeof(unsigned long long));
   if(counts == NULL) 
     exit(EXIT_FAILURE);
 
   while ((read = getline(&line, &len, fh)) != -1) {
     if(line[0] != '>')   {
-
       for(i = 0; i < strlen(line) - kmer; i++) {
         counts[convert_kmer_to_index(&line[i],kmer, width)]++;
       }
-- 
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