Remove singleton sequences from wells in initial filtering

src/main/java/Simulator.java

@@ -46,9 +46,9 @@ public class Simulator implements GraphModificationFunctions {
         if(verbose){System.out.println("All betas count: " + betaCount);}
         if(verbose){System.out.println("Well maps made");}
 
-        if(verbose){System.out.println("Removing sequences present in all wells.");}
+        if(verbose){System.out.println("Removing singleton sequences and sequences present in all wells.");}
-        filterByOccupancyThresholds(allAlphas, 1, numWells - 1);
+        filterByOccupancyThresholds(allAlphas, 2, numWells - 1);
-        filterByOccupancyThresholds(allBetas, 1, numWells - 1);
+        filterByOccupancyThresholds(allBetas, 2, numWells - 1);
         if(verbose){System.out.println("Sequences removed");}
         int pairableAlphaCount = allAlphas.size();
         if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);}
@@ -157,7 +157,6 @@ public class Simulator implements GraphModificationFunctions {
                 "removed");}
 
         //Find Maximum Weighted Matching
-        //using jheaps library class PairingHeap for improved efficiency
         if(verbose){System.out.println("Finding maximum weighted matching");}
         MaximumWeightBipartiteMatching maxWeightMatching;
         //Use correct heap type for priority queue