rename to counts per sequence, don't provide frequencies only counts

1 files changed, 71 insertions, 0 deletions

diff --git a/kmer_counts_per_sequence.c b/kmer_counts_per_sequence.c
new file mode 100644
index 0000000..d518efc
--- /dev/null
+++ b/kmer_counts_per_sequence.c
@@ -0,0 +1,71 @@
+// Copyright 2013 Calvin Morrison
+#include <errno.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "kmer_utils.h"
+
+unsigned long position = 0;
+int main(int argc, char **argv) {
+
+  char *line = NULL;
+  size_t len = 0;
+  ssize_t read;
+
+  if(argc != 3) {
+    printf("Please supply a filename and a kmer\n");
+    exit(EXIT_FAILURE);
+  }
+
+  FILE *fh = fopen(argv[1], "r" );
+  if(fh == NULL) {
+    fprintf(stderr, "Error opening %s - %s\n", argv[1], strerror(errno));
+    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));
+	if(counts == NULL) 
+		exit(EXIT_FAILURE);
+
+  while ((read = getline(&line, &len, fh)) != -1) {
+    if(line[0] != '>' && (read > kmer)) {
+
+      unsigned int i = 0;
+      unsigned long total = 0;
+
+			// reset our count matrix to zero
+			memset(counts, 0, width * sizeof(unsigned long long));
+
+  		for(i = 0; i < read - kmer; i++) {
+				line[i] = alpha[(int)line[i]];
+			}
+
+      for(i = 0; i < read - kmer; i++) {
+        counts[num_to_index(&line[i],kmer, width)]++;
+      }
+
+      for(i = 0; i < width; i++)
+        total += counts[i];
+
+      for(i = 0; i < width - 1; i++)
+        printf("%llu\t", counts[i]);
+      printf("%llu\n", counts[width - 1]);
+
+    }
+  }
+
+	free(counts);
+  free(line);
+
+
+  return EXIT_SUCCESS;
+}