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

1 files changed, 0 insertions, 71 deletions

diff --git a/kmer_frequency_per_sequence.c b/kmer_frequency_per_sequence.c
deleted file mode 100644
index 7b14f6d..0000000
--- a/kmer_frequency_per_sequence.c
+++ /dev/null
@@ -1,71 +0,0 @@
-// 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("%.12f\t", (double)counts[i] / total);
-      printf("%.12f\n", (double)counts[width - 1] / total);
-
-    }
-  }
-
-	free(counts);
-  free(line);
-
-
-  return EXIT_SUCCESS;
-}