830 - MarkovModel::CountErrorsAndRecombinants()

void MarkovModel::CountErrorsAndRecombinants(char * observed, char ** haplotypes, float ** freq)
   {
   float * swap;
   float * vector = new float [states];
   float * extra = new float [states];

   // Initialize likelihoods at first position
   for (int i = 0; i < states; i++)
      vector[i] = 1.;

   // Scan along chromosome
   for (int i = markers - 1; i > 0; i--)
      {
      for (int j = 0; j < states; j++)
         extra[j] = vector[j] * matrix[i][j];

      if (observed[i])
         {
         errorCount[i] += CountErrors(extra, haplotypes, i, observed[i], E[i], freq[observed[i]][i]);
         Condition(vector, haplotypes, i, observed[i], E[i], freq[observed[i]][i]);
         }
      else
         errorCount[i] += E[i];

      recombinantCount[i-1] += CountRecombinants(vector, matrix[i - 1], R[i-1]);

      Transpose(vector, extra, R[i - 1]);
      swap = vector; vector = extra; extra = swap;
      }

   if (observed[0])
      {
      Condition(vector, haplotypes, 0, observed[0], E[0], freq[observed[0]][0]);
      errorCount[0] += CountErrors(vector, haplotypes, 0, observed[0], E[0], freq[observed[0]][0]);
      }
   else
      errorCount[0] += E[0];

   delete [] vector;
   delete [] extra;
   }