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// 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 5
#define SPACE 6
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
bool translate_nucleotides_to_numbers(char *str, size_t len, const unsigned char *lookup, bool start_header) {
bool header = start_header;
size_t i;
for(i = 0; i < len; ++i) {
if(str[i] == '>') {
header = true;
}
if(header) {
if(str[i] == '\n') {
header = false;
}
str[i] = ERROR;
}
else
str[i] = lookup[(int)str[i]];
}
return header;
}
static size_t calculate_mer(const char *str, size_t str_len, size_t *pos, size_t kmer_len, size_t error_mer) {
size_t mer = 0;
size_t multiply;
size_t i;
size_t end;
// set our multiplier to be pow(4, mer) >> 2;
multiply = kmer_pow_four(kmer_len) >> 2;
end = *pos + kmer_len;
// check if space or error, otherwise bump our multiplier and mer
for(i = *pos; i < end; ++i) {
if(str[i] == SPACE) {
// if our end has been expanded to the max string length
// or if it is the first loop return the error length
if(end == str_len || i == *pos)
return error_mer;
end++;
continue;
}
if(str[i] == ERROR) {
*pos = i;
return error_mer;
}
// multiply this char in the mer by the multiply
// and bitshift the multiply for the next round
mer += str[i] * multiply;
multiply = multiply >> 2;
}
return mer;
}
static size_t fread_save_n_bytes(char *buffer, FILE *fh, size_t save_size, size_t buffer_size, size_t len) {
if(ftell(fh) == 0) {
fread(buffer, 1, buffer_size, fh);
len = buffer_size - save_size;
}
else {
size_t read_size = buffer_size - save_size;
memcpy(buffer, buffer + len, save_size);
len = fread(buffer + save_size, 1, read_size, fh);
}
return len;
}
unsigned long long *kmer_counts_from_file(FILE *fh, const unsigned int kmer) {
char buffer[BUFSIZ] = { 0 };
bool header = false;
bool started = false;
size_t len = 0;
size_t position;
const unsigned long width = kmer_pow_four(kmer);
// malloc 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_save_n_bytes(buffer, fh, kmer, BUFSIZ - 1, len)) != NULL) {
size_t i;
char *ptr = buffer;
if(started)
ptr = buffer + kmer;
header = translate_nucleotides_to_numbers(ptr, len, kmer_alpha, header);
for(i = 0; i < (len - kmer + 1); i++) {
size_t mer = calculate_mer(buffer, len, &i, kmer, width);
counts[mer]++;
}
started = true;
}
return counts;
}
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