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// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "kmer_utils.h"
long position = 0;
int main(int argc, char **argv) {
char *line = NULL;
size_t len = 0;
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");
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 = (int)pow(4, kmer);
// malloc our counts matrix
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(position = 0; position < (read - kmer); position++) {
counts[num_to_index(&line[position],kmer, width)]++;
}
}
}
for(i = 0; i < (unsigned)width; i++)
printf("%llu\n", counts[i]);
return EXIT_SUCCESS;
}
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