From 2a831c405c8372f86c22c5cf3684f63209877b49 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Fri, 4 Oct 2013 18:25:21 -0400
Subject: no more branching

---
 kmer_frequency_per_sequence.c | 20 +++++++++++++++++---
 kmer_total_count.c            | 34 ++++++++++++++++++++++++----------
 kmer_total_count.h            |  2 +-
 kmer_utils.c                  |  7 ++-----
 4 files changed, 44 insertions(+), 19 deletions(-)

diff --git a/kmer_frequency_per_sequence.c b/kmer_frequency_per_sequence.c
index aa18dd6..02a221b 100644
--- a/kmer_frequency_per_sequence.c
+++ b/kmer_frequency_per_sequence.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) {
 
@@ -31,14 +43,16 @@ int main(int argc, char **argv) {
   width = (int)pow(4, kmer);
 
   while ((read = getline(&line, &len, fh)) != -1) {
-    if(line[0] != '>' && read > kmer) {
+    if(line[0] != '>' && (read > kmer)) {
 
       unsigned int i = 0;
       unsigned long long *counts = malloc((width+ 1) * sizeof(unsigned long long));
       if(counts == NULL) 
         exit(EXIT_FAILURE);
 
-      convert_kmer_to_num(line, read);
+  		for(i = 0; i < read - kmer; i++) {
+				line[i] = alpha[line[i]];
+			}
 
       for(i = 0; i < read - kmer; i++) {
         counts[num_to_index(&line[i],kmer, width)]++;
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;
diff --git a/kmer_total_count.h b/kmer_total_count.h
index e782906..0c3d12d 100644
--- a/kmer_total_count.h
+++ b/kmer_total_count.h
@@ -1 +1 @@
-extern long position;
+extern unsigned long position;
diff --git a/kmer_utils.c b/kmer_utils.c
index f4f8d2f..a1ff9b2 100644
--- a/kmer_utils.c
+++ b/kmer_utils.c
@@ -2,7 +2,7 @@
 
 // convert a string of k-mer size base-4 values  into a
 // base-10 index
-unsigned long num_to_index(const char *str, const int kmer, const long error_pos) {
+inline unsigned long num_to_index(const char *str, const int kmer, const long error_pos) {
 
   int i = 0;
   unsigned long out = 0;
@@ -17,7 +17,6 @@ unsigned long num_to_index(const char *str, const int kmer, const long error_pos
 			return error_pos;
 		}
 
-
     out += str[i] * multiply;
     multiply = multiply << 2;
   }
@@ -25,9 +24,6 @@ unsigned long num_to_index(const char *str, const int kmer, const long error_pos
   return out;
 }
 
-// replaces values in a char array of ACGT's and others with
-// values that correspond to their base 4 value to be used in
-// num_to_index.
 void convert_kmer_to_num(char *str, const unsigned long length) {
 
   unsigned long i = 0;
@@ -56,3 +52,4 @@ void convert_kmer_to_num(char *str, const unsigned long length) {
   }
 
 }
+
-- 
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