works with multiline sequences, abstracted most code to kmer_utils.c

1 files changed, 7 insertions, 65 deletions

diff --git a/kmer_total_count.c b/kmer_total_count.c
index 795b5dc..34abfa0 100644
--- a/kmer_total_count.c
+++ b/kmer_total_count.c
@@ -5,80 +5,22 @@
 #include <string.h>
 
 #include "kmer_utils.h"
-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) {
 
-  char *line = NULL;
-  size_t len = 0;
-  ssize_t read;
-  long i = 0;
-	long posistion = 0;
+  unsigned long long i = 0;
 
-  if(argc != 3) {
+  if(argc !=  3) {
     printf("Please supply a filename and a kmer\n");
     exit(EXIT_FAILURE);
   }
 
-  FILE * const fh = fopen(argv[1], "r");
-  if(fh == NULL) {
-    fprintf(stderr, "Error opening %s - %s\n", argv[1], strerror(errno));
-    exit(EXIT_FAILURE);
-  }
-
-  // second argument is the kmer
-  const unsigned int kmer = atoi(argv[2]);
-
-  // width is 4^kmer 
-	const unsigned long width = (unsigned long)1 << (kmer * 2);
-
-  // malloc our counts matrix
-  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) {
-
-  		for(i = 0; i < read; i++) {
-				line[i] = alpha[line[i]];
-			}
-
-      for(posistion = 0; posistion < (read - kmer); posistion++) {
-				unsigned long out = 0;
-				unsigned long multiply = 1;
-				
-
-				for(i = posistion + kmer - 1; i >= posistion; i--){
-					if(line[i] >> 2) { 
-						out = width;
-						posistion = i;
-						goto next;
-					}
-
-					out += line[i] * multiply;
-					multiply = multiply << 2;
-				}
-				next:
-        counts[out]++;
-      }
-    } 
-  }
-
-  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]);
+	unsigned long long *counts = get_kmer_counts_from_file(argv[1], atoi(argv[2]));
 
+	// print out our counts arrray
+	// manually unrolled 4 loops to reduce fprintf calls
+  for(i = 0; i < pow_four(atoi(argv[2])); i=i+4)
+    fprintf(stdout, "%llu\n%llu\n%llu\n%llu\n", counts[i], counts[i+1], counts[i+2], counts[i+3]);
 
   return EXIT_SUCCESS;
 }