1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
|
// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "kmer_utils.h"
int main(int argc, char **argv) {
unsigned long long i = 0;
long long j = 0;
if(argc < 3) {
fprintf(stderr, "Please supply a filename and a kmer, then as many kmers as you want (in ACGT format)\n");
exit(EXIT_FAILURE);
}
unsigned long kmer = atoi(argv[2]);
unsigned long long width = pow_four(kmer);
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
// manually unrolled 4 loops to reduce fprintf calls
if(argc == 3) {
for(i = 0; i < width; i=i+4)
fprintf(stdout, "%llu\n%llu\n%llu\n%llu\n", counts[i], counts[i+1], counts[i+2], counts[i+3]);
}
else {
for(i = 3; i < argc; i++) {
unsigned long k = width;
size_t len = 0;
fprintf(stdout, "%s\t", argv[i]);
len = strlen(argv[i]);
if(len != kmer) {
fprintf(stdout, "ERR\n");
continue;
}
for(j = 0; j < len; j++)
argv[i][j] = alpha[argv[i][j]];
k = num_to_index(argv[i], kmer, width);
if(k == width) {
fprintf(stdout, "ERR\n");
}
else {
fprintf(stdout, "%llu\n", counts[k]);
}
}
}
return EXIT_SUCCESS;
}
|
