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

1 files changed, 5 insertions, 9 deletions

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: