//DD_BS_Setup_Reference_Arrays
  //RAM, Nov 1, 2015
// put all the imported data into arrays from the table records to make it go faster

  //arrays of allele positions
ALL RECORDS([Alleles])
SELECTION TO ARRAY([Alleles]Allel_label;aAllele;[Alleles]Locus;aLocus;[Alleles]Orig_Position;aOPos)
ARRAY INTEGER(aNewPos;Size of array(aOPos))
ARRAY REAL(aRand1;Size of array(aOPos))

  //Which indiv do you want?
$Type:="Big_A@"
  //indivdiuals with alleles
QUERY([Individuals];[Individuals]Phase=$Type)
SELECTION TO ARRAY([Individuals]ID;aID;[Individuals]L1A1;aL11;[Individuals]L1A2;aL12;[Individuals]L2A1;aL21;[Individuals]L2A2;aL22)

  //the
$N:=Size of array(aID)

ARRAY INTEGER(aLoc11;$N)
ARRAY INTEGER(aLoc12;$N)
ARRAY INTEGER(aLoc21;$N)
ARRAY INTEGER(aLoc22;$N)

ARRAY INTEGER(aL1_ID;11)
ARRAY INTEGER(aL1_Loc;11)
ARRAY REAL(aL1_Rand;11)

ARRAY INTEGER(aL2_ID;13)
ARRAY INTEGER(aL2_Loc;13)
ARRAY REAL(aL2_Rand;13)


$N:=Size of array(aOPos)

  //get the Locus 1 locations and the Locus 2 lcoations
For ($i;1;$N)

     If ($i<12)  //L1 location

          aL1_ID{$i}:=aAllele{$i}
          aL1_Loc{$i}:=aOPos{$i}

     Else 

          aL2_ID{$i-11}:=aAllele{$i}
          aL2_Loc{$i-11}:=aOPos{$i}


     End if 
End for