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#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
// convert a string of k-mer size base-4 values into a
// base-10 index
long num_to_index(const char *str, const int kmer, const long error_pos) {
int i = 0;
unsigned long out = 0;
unsigned long multiply = 1;
for(i = kmer - 1; i >= 0; i--){
if(str[i] >> 2)
return error_pos;
out += str[i] * multiply;
multiply = multiply << 2;
}
return out;
}
// replaces values in a char array of ACGT's and others with
// values that correspond to their base 4 value to be used in
// num_to_index.
void convert_kmer_to_num(char *str, const long length) {
long i = 0;
for(i = 0; i < length; i++) {
// this is _not_ portable, only works with ASCII values.
switch(str[i] | 0x20 ) {
case 'a':
str[i] = 0;
break;
case 'c':
str[i] = 1;
break;
case 'g':
str[i] = 2;
break;
case 't':
str[i] = 3;
break;
default:
// Error Checking: use 4 so we can shift right twice
// to check quickly is there is an non ACGT character
str[i] = 4;
}
}
}
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