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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(char *str, unsigned long kmer, long error_pos) {
char **ptr = NULL;
char vals[kmer];
unsigned long i = 0;
for(i = 0; i < kmer; i++) {
switch(str[i]) {
case 'a':
case 'A':
vals[i] = '0';
break;
case 'c':
case 'C':
vals[i] = '1';
break;
case 'g':
case 'G':
vals[i] = '2';
break;
case 't':
case 'T':
vals[i] = '3';
break;
default:
return error_pos;
}
}
return strtol(vals, ptr, 4);
}
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