From 8d1e990611a128d123e47f8a068ff9b045794db4 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Sat, 14 Sep 2013 12:58:13 -0400
Subject: improve performance of convert_kmer_to_index by using a bitwise OR to
 convert our characters to lowercare: str[i] | Ox20, and reduce the number of
 switches as a result

---
 kmer_total_count.c |  3 ++-
 kmer_utils.c       | 14 +++++---------
 2 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/kmer_total_count.c b/kmer_total_count.c
index 23ca512..6d07e13 100644
--- a/kmer_total_count.c
+++ b/kmer_total_count.c
@@ -13,8 +13,9 @@ int main(int argc, char **argv) {
   char *line = NULL;
   size_t len = 0;
   ssize_t read;
+  long i = 0;
+
   unsigned int kmer = 0;
-  unsigned long i = 0;
   unsigned long width = 0;
   unsigned long long *counts;
 
diff --git a/kmer_utils.c b/kmer_utils.c
index e737346..c0441e2 100644
--- a/kmer_utils.c
+++ b/kmer_utils.c
@@ -16,27 +16,23 @@
 //  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, long kmer, long error_pos) {
+inline long convert_kmer_to_index(const char *str, int kmer, long error_pos) {
 
-  long i = 0;
-  long out = 0;
-  long multiply = 1;
+  int i = 0;
+  unsigned long out = 0;
+  unsigned long multiply = 1;
 
   for(i = kmer - 1; i >= 0; i--){
-    switch(str[i]) {
+    switch(str[i] | 0x20 ) {
       case 'a':
-      case 'A':
         break;
       case 'c':
-      case 'C':
         out += 1 * multiply;
         break;
       case 'g':
-      case 'G':
         out += 2 * multiply;
         break;
       case 't':
-      case 'T':
         out += 3 * multiply;
         break;
       default:
-- 
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