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
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
|
// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <stdbool.h>
#include "kmer_total_count.h"
#define ERROR_CODE 5
#define SPACE_CODE 6
#define BUFFER_SIZE 256
const unsigned char kmer_alpha[256] =
// \n
{5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
// > A C G
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,
// T A C G
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,
// T
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};
static const char reverse_alpha[4] = { 'A', 'C', 'G', 'T' };
unsigned long long kmer_pow_four(unsigned long long x) {
return 1ULL << (x * 2);
}
// convert an index back into a kmer string
char *kmer_index_to_kmer(unsigned long long index, long kmer) {
int i = 0;
int j = 0;
char *num_array = calloc(kmer, sizeof(char));
char *ret = calloc(kmer + 1, sizeof(char));
if(ret == NULL)
exit(EXIT_FAILURE);
// this is the core of the conversion. modulus 4 for base 4 conversion
while (index != 0) {
num_array[i] = index % 4;
index /= 4;
i++;
}
// for our first few nmers, like AAAAA, the output would only be "A" instead
// of AAAAA so we prepend it
for(j = 0; j < (kmer - i); j++)
ret[j] = 'A';
// our offset for how many chars we prepended
int offset = j;
// save i so we can print it
int start = i ;
// decrement i by 1 to reverse the last i++
i--;
j = 0;
// reverse the array, as j increases, decrease i
for(j = 0; j < start; j++, i--)
ret[j + offset] = reverse_alpha[(int)num_array[i]];
// set our last character to the null termination byte
ret[kmer + 1] = '\0';
free(num_array);
return ret;
}
// convert a string into values from a lookup array
size_t translate_nucleotides_to_numbers(char *str, size_t len, const unsigned char *lookup) {
size_t i = 0;
for(i = 0; i < len; ++i) {
if(str[i] == '>') {
return i;
}
else {
str[i] = lookup[(int)str[i]];
}
}
return i;
}
static int is_whitespace(char c) {
return c == SPACE_CODE;
}
static int is_error_char(char c) {
return c == ERROR_CODE;
}
static size_t calculate_mer(const char *str, size_t *pos, size_t kmer_len, size_t error_mer) {
size_t mer = 0;
size_t multiply = 1;
size_t i;
/* printf("-----\n"); */
// for each char in the k-mer check if it is an error char
for(i = *pos; i < *pos + kmer_len; ++i) {
if(is_whitespace(str[i])) {
continue;
}
if(is_error_char(str[i])) {
mer = error_mer;
*pos = i;
return mer;
}
// multiply this char in the mer by the multiply
// and bitshift the multiply for the next round
/* printf("str[i] = %d\n", str[i]); */
/* printf("i = %zu\n", i); */
mer += str[i] * multiply;
multiply = multiply << 2;
/* printf("mer - %zu\n", mer); */
}
return mer;
}
size_t consume_header(const char *str, size_t len) {
size_t i;
for(i = 0; i < len; ++i) {
if(str[i] == '\n') {
++i;
return i;
}
}
return len;
}
unsigned long long *kmer_counts_from_file(FILE *fh, const unsigned int kmer) {
char buffer[BUFFER_SIZE] = { 0 };
char *start = buffer;
size_t read_len = BUFFER_SIZE;
bool in_header = false;
size_t len = 0;
const unsigned long width = kmer_pow_four(kmer);
// calloc our return array
unsigned long long *counts = calloc(width + 1, sizeof *counts);
if(counts == NULL) {
fprintf(stderr, strerror(errno));
exit(EXIT_FAILURE);
}
while((len = fread(start, 1, read_len, fh)) != 0) {
size_t total_len = (start + len) - buffer;
size_t processed = 0;
printf("total_len = %zu\n", total_len);
while(processed != total_len) {
printf("processed = %zu\n", processed);
if(in_header) {
processed += consume_header(buffer + processed, total_len - processed);
in_header = (processed == total_len);
}
in_header = in_header || buffer[processed] == '>';
if(!in_header) {
size_t i;
size_t to_process = processed;
to_process += translate_nucleotides_to_numbers(buffer + processed, total_len, kmer_alpha);
for(i = processed; i < (to_process - kmer + 1); ++i) {
size_t mer = calculate_mer(buffer, &i, kmer, width);
counts[mer]++;
}
processed = to_process;
in_header = (buffer[processed] == '>');
}
}
memcpy(buffer, buffer + processed, processed);
start = buffer + (BUFFER_SIZE - processed);
read_len = BUFFER_SIZE - (start - buffer);
}
return counts;
}
|
