Mixed starting strain to one ending strain

I run a small mouse speed congenics facility.   I use microsatellite analysis to find the highest percent mouse for each generation. Panels of multiplexed primers are used to distinguish between one inbred mouse strain and the other.  The panels include primers that are polymorphic between the two inbred mouse strains. Each panel has been tested for multiplexing and includes up to 3 fluorescencly labeled primer sets in each well.  The entire system is set up to run in a 96 well format.     

I get many different types of projects and my panels are set up to go from one starting inbred mouse strain to one ending inbred mouse strain.  The function will returns a file containing a multiplexed plate or plates that needs to run that includes all the primers missing in the first plate but present in the second plate.

Example use of this function:

   |       A customer comes to start a speed congenics project however the

   |       starting strain of the project is mixed.  For example the starting

   |       strain is 129 and C3H combined.  The customer wants to cross this

   |       mouse onto the B6 background.  Therefore the best approach would be

   |       to run a full 129XB6 screen and then run the primers that are present

   |       in the B6XC3H screen and not in the 129XB6 screen.

       

here's the code