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
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
|
// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "kmer_utils.h"
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;
long posistion = 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 = (unsigned long)1 << (kmer * 2);
// 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(posistion = 0; posistion < (read - kmer); posistion++) {
unsigned long out = 0;
unsigned long multiply = 1;
for(i = posistion + kmer - 1; i >= posistion; i--){
if(line[i] >> 2) {
out = width;
posistion = i;
goto next;
}
out += line[i] * multiply;
multiply = multiply << 2;
}
next:
counts[out]++;
}
}
}
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;
}
|
