830 - Haplotyper::ScoreLeftConditional() (smart, complicated)

// This version of the ScoreLeftConditional() function deals with sites
// where no genotypes are observed a little more efficiently.
//

void Haplotyper::ScoreLeftConditional()
   {
   ResetMemoryPool();
   GetMemoryBlock(0);

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

   double theta = 0.0;
   float *from = leftMatrices[0];
   for (int i = 1; i < markers; i++)
      {
      // Cumulative recombination fraction allows us to skip uninformative positions
      theta = theta + thetas[i - 1] - theta * thetas[i - 1];

      // Skip over uninformative positions to save time
      if (current_genotypes[i] != GENOTYPE_MISSING || i == markers - 1)
         {
         GetMemoryBlock(i);

         Transpose(from, leftMatrices[i], theta);
         ConditionOnData(leftMatrices[i], i, current_genotypes[i]);

         theta = 0;
         from = leftMatrices[i];
         }
      }
   }