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// Copyright 2013 Calvin Morrison
#include <errno.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unordered_map>
using namespace std;
typedef struct {
size_t operator() (const size_t &k) const {
return k;
}
} kmer_noHash_hash;
typedef struct {
bool operator() (const size_t &x, const size_t &y) const {
return x == y;
}
} kmer_eq;
typedef unordered_map<size_t, unsigned long long, kmer_noHash_hash, kmer_eq> kmer_map;
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};
const char reverse_alpha[4] = { 'A', 'C', 'G', 'T' };
unsigned long long pow_four(unsigned long long x) {
return (unsigned long long)1 << (x * 2);
}
// convert a string of k-mer size base-4 values into a
// base-10 index
unsigned long num_to_index(const char *str, const int kmer, const long error_pos, long long *current_position) {
int i = 0;
unsigned long out = 0;
unsigned long multiply = 1;
for(i = kmer - 1; i >= 0; i--){
if(str[i] == 5) {
current_position += i;
return error_pos;
}
out += str[i] * multiply;
multiply = multiply << 2;
}
return out;
}
// return the number of loaded elements
size_t load_specific_mers_from_file(char *fn, unsigned int kmer, size_t width, size_t *arr) {
FILE *fh;
size_t arr_pos = 0;
char line[64];
fh = fopen(fn, "r");
if(fh == NULL) {
fprintf(stderr, "Error opening %s - %s\n", fn, strerror(errno));
exit(EXIT_FAILURE);
}
while (fgets(line, sizeof(line), fh) != NULL) {
size_t i;
size_t len;
len = strlen(line);
if(len == 0)
continue;
len--;
line[len] = '\0';
if(len != kmer) {
fprintf(stderr, "SKIPPING: '%s' is not length %u\n", line, kmer);
continue;
}
for(i = 0; i < len; i++) {
line[i] = alpha[(int)line[i]];
}
size_t mer = num_to_index(line, kmer, width, NULL);
if(mer == width) {
fprintf(stderr, "SKIPPING: '%s' is a unrecognized mer\n", line);
continue;
}
else {
arr[arr_pos] = mer;
arr_pos++;
}
}
fclose(fh);
return arr_pos;
}
// convert an index back into a kmer string
char *index_to_kmer(unsigned long long index, long kmer) {
size_t i = 0;
size_t j = 0;
char *num_array = (char *) calloc(kmer, sizeof(char));
char *ret = (char *) calloc(kmer + 1, sizeof(char));
if(ret == NULL || num_array == 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
size_t 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;
}
// Strip out any character 'c' from char array 's'
// returns length of new string
size_t strnstrip(char *s, int c, size_t len) {
size_t i = 0;
size_t j = 0;
for(i = 0; i < len; i++) {
if(s[i] != c) {
if(j != i)
s[j] = s[i];
j++;
}
}
s[j] = '\0';
return j;
}
kmer_map *get_sparse_kmer_counts_from_file(FILE *fh, int kmer) {
char *line = NULL;
size_t len = 0;
ssize_t read;
long long i = 0;
long long position = 0;
kmer_map *counts = new kmer_map();
//
// width is 4^kmer
const unsigned long long width = pow_four(kmer);
while ((read = getdelim(&line, &len, '>', fh)) != -1) {
size_t k;
char *seq;
size_t seq_length;
// find our first \n, this should be the end of the header
seq = strchr(line, '\n');
if(seq == NULL)
continue;
// point to one past that.
seq = seq + 1;
// strip out all other newlines to handle multiline sequences
strnstrip(seq, '\n', strlen(seq));
seq_length = strlen(seq);
// relace A, C, G and T with 0, 1, 2, 3 respectively
// everything else is 5
for(k = 0; k < seq_length; k++)
seq[k] = alpha[(int)seq[k]];
// loop through our seq to process each k-mer
for(position = 0; position < (signed)(seq_length - kmer + 1); position++) {
unsigned long long mer = 0;
unsigned long long multiply = 1;
// for each char in the k-mer check if it is an error char
for(i = position + kmer - 1; i >= position; i--){
if(seq[i] == 5) {
position = i;
goto next;
}
// multiply this char in the mer by the multiply
// and bitshift the multiply for the next round
mer += seq[i] * multiply;
multiply = multiply << 2;
}
// bump up the mer value in the counts array
(*counts)[mer]++;
next: ;
}
}
free(line);
fclose(fh);
return counts;
}
unsigned long long * get_dense_kmer_counts_from_file(FILE *fh, const unsigned int kmer) {
char *line = NULL;
size_t len = 0;
ssize_t read;
long long i = 0;
long long position = 0;
// width is 4^kmer
const unsigned long long width = pow_four(kmer);
unsigned long long *counts = (unsigned long long *) calloc(width+1, sizeof(unsigned long long));
if(counts == NULL) {
exit(EXIT_FAILURE);
}
while ((read = getdelim(&line, &len, '>', fh)) != -1) {
size_t k;
char *seq;
size_t seq_length;
// find our first \n, this should be the end of the header
seq = strchr(line, '\n');
if(seq == NULL)
continue;
// point to one past that.
seq = seq + 1;
// strip out all other newlines to handle multiline sequences
strnstrip(seq, '\n', strlen(seq));
seq_length = strlen(seq);
// relace A, C, G and T with 0, 1, 2, 3 respectively
// everything else is 5
for(k = 0; k < seq_length; k++)
seq[k] = alpha[(int)seq[k]];
// loop through our seq to process each k-mer
for(position = 0; position < (signed)(seq_length - kmer + 1); position++) {
unsigned long long mer = 0;
unsigned long long multiply = 1;
// for each char in the k-mer check if it is an error char
for(i = position + kmer - 1; i >= position; i--){
if(seq[i] == 5) {
position = i;
goto next;
}
// multiply this char in the mer by the multiply
// and bitshift the multiply for the next round
mer += seq[i] * multiply;
multiply = multiply << 2;
}
// bump up the mer value in the counts array
counts[mer]++;
next: ;
}
}
//free(line);
fclose(fh);
return counts;
}
unsigned long long * get_dense_kmer_counts_from_filename(const char *fn, const unsigned int kmer) {
FILE *fh = fopen(fn, "r");
if(fh == NULL) {
fprintf(stderr, "Could not open %s - %s\n", fn, strerror(errno));
return 0;
}
return get_dense_kmer_counts_from_file(fh, kmer);
}
void print_kmer(unsigned long long *counts, bool label, bool nonzero, unsigned int kmer) {
size_t width = pow_four(kmer);
size_t i = 0;
// 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 = 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, "%zu\t%llu\n", i, counts[i]);
}
}
// If we aren't printing nonzeros print everything
else {
if(label) {
for(i = 0; i < width; i++) {
char *kmer_str = 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]);
}
}
}
}
void print_kmer(kmer_map *counts, bool label, bool nonzero, unsigned int kmer) {
size_t width = pow_four(kmer);
size_t i = 0;
// If nonzero is set, only print non zeros
if(nonzero) {
// if labels is set, print out our labels
if(label) {
for(auto it = counts->begin(); it != counts->end(); it++ ) {
char *kmer_str = index_to_kmer(it->first, kmer);
fprintf(stdout, "%s\t%llu\n", kmer_str, it->second);
free(kmer_str);
}
}
else {
for(auto it = counts->begin(); it != counts->end(); it++ ) {
fprintf(stdout, "%zu\t%llu\n", it->first, it->second);
}
}
}
// If we aren't printing nonzeros print everything
else {
if(label) {
for(i = 0; i < width; i++) {
char *kmer_str = index_to_kmer(i, kmer);
if(counts->count(i) != 0)
fprintf(stdout, "%s\t%llu\n", kmer_str, counts->at(i));
else
fprintf(stdout, "%s\t0\n", kmer_str);
free(kmer_str);
}
}
else {
for(i = 0; i < width; i++) {
if(counts->count(i) != 0)
fprintf(stdout, "%llu\n", counts->at(i));
else
fprintf(stdout, "0\n");
}
}
}
}
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