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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"
unsigned long position = 0;
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;
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 = pow(4, kmer);
// 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(position = 0; position < (read - kmer); position++) {
counts[num_to_index(&line[position],kmer, width)]++;
}
}
}
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]);
return EXIT_SUCCESS;
}
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