reorder kmer_utils.h, actually take a kmer value as argv[2] for frequency, error check kmer

3 files changed, 15 insertions, 4 deletions

diff --git a/kmer_frequency_per_sequence.c b/kmer_frequency_per_sequence.c
index d3e21a1..7c1bf9b 100644
--- a/kmer_frequency_per_sequence.c
+++ b/kmer_frequency_per_sequence.c
@@ -10,7 +10,6 @@ unsigned long position = 0;
 int main(int argc, char **argv) {
 
   char *line = NULL;
-  long kmer = 6;
   size_t len = 0;
   ssize_t read;
 
@@ -25,6 +24,12 @@ int main(int argc, char **argv) {
     exit(EXIT_FAILURE);
   }
 
+	unsigned long kmer = atoi(argv[2]);
+	if(kmer == 0) { 
+		fprintf(stderr, "Error: invalid kmer.\n");
+		exit(EXIT_FAILURE);
+	}
+
 	const unsigned long width = (unsigned long)1 << (kmer * 2);
 
 	unsigned long long *counts = malloc((width+ 1) * sizeof(unsigned long long));
@@ -41,7 +46,7 @@ int main(int argc, char **argv) {
 			memset(counts, 0, width);
 
   		for(i = 0; i < read - kmer; i++) {
-				line[i] = alpha[line[i]];
+				line[i] = alpha[(int)line[i]];
 			}
 
       for(i = 0; i < read - kmer; i++) {
diff --git a/kmer_total_count.c b/kmer_total_count.c
index 34abfa0..ec9a3f8 100644
--- a/kmer_total_count.c
+++ b/kmer_total_count.c
@@ -11,10 +11,16 @@ int main(int argc, char **argv) {
   unsigned long long i = 0;
 
   if(argc !=  3) {
-    printf("Please supply a filename and a kmer\n");
+    fprintf(stderr, "Please supply a filename and a kmer\n");
     exit(EXIT_FAILURE);
   }
 
+	unsigned long kmer = atoi(argv[2]);
+	if(kmer == 0) { 
+		fprintf(stderr, "Error: invalid kmer.\n");
+		exit(EXIT_FAILURE);
+	}
+
 	unsigned long long *counts = get_kmer_counts_from_file(argv[1], atoi(argv[2]));
 
 	// print out our counts arrray
diff --git a/kmer_utils.h b/kmer_utils.h
index 11506b3..4ed5928 100644
--- a/kmer_utils.h
+++ b/kmer_utils.h
@@ -1,4 +1,4 @@
-// kmer functions
+// Kmer functions
 void convert_kmer_to_num(char *str, const unsigned long length);
 unsigned long num_to_index(const char *str, const int kmer, const long error_pos);
 unsigned long long * get_kmer_counts_from_file(const char *fn, const int kmer);