I tried to create a function to extract SNP from fasta file witch content alignments sequences. Well, I create a function that make statistics for a list of N aligned sequences. Using Rcpp api, the code is:

// [[Rcpp::export]]
 NumericMatrix alin_stat(CharacterVector &alin,int &N_sequence)
   {
   int sequence_size=alin[0].size();
   NumericMatrix stat_m (5,sequence_size);   // set at 0 by default

   for(int i=0;i<N_sequence;i++){

     for(int j=0;j<sequence_size;j++){
       switch (alin[i][j]){

       case 'A' : case 'a':    // first row store the frequency of A
         stat_m(0,j)++;
         break;
       case 'C' : case 'c':    // second row store the frequency of C
         stat_m(1,j)++;
         break;
       case 'G' : case 'g':    // third row store the frequency of G
         stat_m(2,j)++;
         break;
       case 'T' : case 't':    // forth row store the frequency of G
         stat_m(3,j)++;
         break;
         default:
         stat_m(4,j)++;        // non identified base '-','N'...
         break;
       }

     }
   }
  return stat_m/N_sequence; 
 }

Note that:

alin contains aligned sequences

N_sequence is number of sequences

Question:

• Witch condition I have to rich to select an SNP?
• Is the alignment procedure (parameters) affects the target result?