830 - Haplotyper::ImputeGenotypes()

void Haplotyper::ImputeGenotypes()
   {
   RewindMemoryPool();

   // Process the last position
   RetrieveMemoryBlock(markers - 1);
   ImputeGenotypes(leftMatrices[markers - 1], markers - 1);

   SetupPrior(rightMatrices[0]);
   ConditionOnData(rightMatrices[0], 0, current_genotypes[0]);

   float *temp;
   float *from = rightMatrices[0];
   float *to = rightMatrices[1];

   for (int i = markers - 2; i >= 0; i--)
      {
      // Move things along
      Transpose(from, to, thetas[i]);

      // Find nearest informative marker
      double theta = 0.0;
      int left = i;

      while (left > 0 && genotypes[states / 2][left] == GENOTYPE_MISSING)
         {
         // Cumulative recombination fraction to nearest marker
         theta = theta + thetas[left - 1] - theta * thetas[left - 1];
         left--;
         }

      RetrieveMemoryBlock(left);
      float * leftMatrix = leftMatrices[left];

      if (left != i)
         {
         Transpose(leftMatrix, from, theta);
         leftMatrix = from;
         }

      ImputeGenotypes(leftMatrix, to, i);
      ConditionOnData(to, i, genotypes[states / 2][i]);

      temp = from;
      from = to;
      to = temp;
      }
   }