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
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
|
// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <stdbool.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <getopt.h>
#include "kmer_utils.h"
int main(int argc, char **argv) {
char *filename = NULL;
FILE *fh;
unsigned int kmer = 0;
bool nonzero = 0;
bool label = 0;
bool kmer_set = 0;
unsigned long long width = 0;
unsigned long long i = 0;
static struct option long_options[] = {
{"input", required_argument, 0, 'i'},
{"kmer", required_argument, 0, 'k'},
{"nonzero", no_argument, 0, 'n'},
{"label", no_argument, 0, 'l'},
{"help", no_argument, 0, 'h'},
{0, 0, 0, 0}
};
while (1) {
int option_index = 0;
int c = 0;
c = getopt_long (argc, argv, "i:k:nlvh", long_options, &option_index);
if (c == -1)
break;
switch (c) {
case 'i':
filename = optarg;
break;
case 'k':
kmer = atoi(optarg);
kmer_set = true;
break;
case 'n':
nonzero = true;
break;
case 'l':
label = true;
break;
case 'h':
printf("help-text\n");
exit(EXIT_SUCCESS);
default:
break;
}
}
if(filename == NULL) {
fprintf(stderr, "Error: filename (-i) must be supplied\n");
exit(EXIT_FAILURE);
}
if(kmer == 0 && !kmer_set) {
fprintf(stderr, "Error: kmer (-k) must be supplied\n");
exit(EXIT_FAILURE);
}
if(kmer == 0) {
fprintf(stderr, "Error: invalid kmer - '%d'.\n", kmer);
exit(EXIT_FAILURE);
}
fh = fopen(filename, "r");
if(fh == NULL) {
fprintf(stderr, "Could not open %s\n", filename);
exit(EXIT_FAILURE);
}
width = kmer_pow_four(kmer);
unsigned long long *counts = kmer_counts_from_file(fh, kmer);
// If nonzero is set, only print non zeros
if(nonzero) {
// if labels is set, print out our labels
if(label) {
for(i = 0; i < width; i++)
if(counts[i] != 0) {
char *kmer_str = kmer_index_to_kmer(i, kmer);
fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]);
free(kmer_str);
}
}
else {
for(i = 0; i < width; i++)
if(counts[i] != 0)
fprintf(stdout, "%llu\t%llu\n", i, counts[i]);
}
}
// If we aren't printing nonzeros print everything
else {
if(label) {
for(i = 0; i < width; i++) {
if(counts[i] != 0) {
char *kmer_str = kmer_index_to_kmer(i, kmer);
fprintf(stdout, "%s\t%llu\n", kmer_str, counts[i]);
free(kmer_str);
}
}
}
else {
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]);
}
}
}
free(counts);
return EXIT_SUCCESS;
}
|
