From 4d00f90fd8b1b9e38eea297336ee83a5e5c9e764 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Sat, 28 Sep 2013 11:52:45 -0700
Subject: idea

---
 kmer_frequency_per_sequence.c |  4 +++-
 kmer_total_count.c            |  4 +++-
 kmer_utils.c                  | 26 +++++++++++++++++++-------
 3 files changed, 25 insertions(+), 9 deletions(-)

diff --git a/kmer_frequency_per_sequence.c b/kmer_frequency_per_sequence.c
index 5191b86..8f0d6b0 100644
--- a/kmer_frequency_per_sequence.c
+++ b/kmer_frequency_per_sequence.c
@@ -37,8 +37,10 @@ int main(int argc, char **argv) {
       if(counts == NULL) 
         exit(EXIT_FAILURE);
 
+      convert_kmer_to_num(line, read);
+
       for(i = 0; i < read - kmer; i++) {
-        counts[convert_kmer_to_index(&line[i], kmer, width)]++;
+        counts[num_to_index(&line[i],kmer, width)]++;
       }
 
       unsigned long total = 0;
diff --git a/kmer_total_count.c b/kmer_total_count.c
index 6d07e13..2416bfa 100644
--- a/kmer_total_count.c
+++ b/kmer_total_count.c
@@ -43,8 +43,10 @@ int main(int argc, char **argv) {
 
   while ((read = getline(&line, &len, fh)) != -1) {
     if(line[0] != '>') {
+      convert_kmer_to_num(line, read);
+
       for(i = 0; i < read - kmer; i++) {
-        counts[convert_kmer_to_index(&line[i],kmer, width)]++;
+        counts[num_to_index(&line[i],kmer, width)]++;
       }
     } 
   }
diff --git a/kmer_utils.c b/kmer_utils.c
index c0441e2..7b483ea 100644
--- a/kmer_utils.c
+++ b/kmer_utils.c
@@ -16,31 +16,43 @@
 //  long kmer - how long of a index value you want to return
 //  long error_pos - what index to return for a non ACGT character
 //
-inline long convert_kmer_to_index(const char *str, int kmer, long error_pos) {
+inline long num_to_index(const char *str, int kmer, long error_pos) {
 
   int i = 0;
   unsigned long out = 0;
   unsigned long multiply = 1;
 
   for(i = kmer - 1; i >= 0; i--){
+
+    out += str[i] * multiply;
+    multiply = multiply << 2;
+  }
+
+  return out;
+}
+
+void convert_kmer_to_num(char *str, long length) {
+
+  long i = 0;
+
+  for(i = 0; i < length; i++) {
     switch(str[i] | 0x20 ) {
       case 'a':
+        str[i] = 0;
         break;
       case 'c':
-        out += 1 * multiply;
+        str[i] = 1;
         break;
       case 'g':
-        out += 2 * multiply;
+        str[i] = 2;
         break;
       case 't':
-        out += 3 * multiply;
+        str[i] = 3;
         break;
       default:
-        return error_pos; 
+        str[i] = 5;
     }
 
-    multiply = multiply << 2;
   }
 
-  return out;
 }
-- 
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