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#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
// This function takes a char array containing sequences and converts it
// into a kmer index (essentially a base 4 radix converstion to base 10, with
// some mumbo-jumbo of taking each of the characters we want (ACGT) and turning
// them into a radix-4 number we can use.
//
// kind of convoluted but it works.
//
// Arguemnts:
// char *str - a NULL terminated character array
// long kmer - how long of a index value you want to return
// long error_pos - what index to return for a non ACGT character
//
inline long convert_kmer_to_index(const char *str, long kmer, long error_pos) {
long i = 0;
long out = 0;
long multiply = 1;
for(i = kmer - 1; i >= 0; i--){
switch(str[i]) {
case 'a':
case 'A':
break;
case 'c':
case 'C':
out += 1 * multiply;
break;
case 'g':
case 'G':
out += 2 * multiply;
break;
case 't':
case 'T':
out += 3 * multiply;
break;
default:
return error_pos;
}
multiply = multiply << 2;
}
return out;
}
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