From 58d418e44b5db7e91e686d393a7b073f488b2b4f Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Sun, 25 Sep 2022 15:06:46 -0500
Subject: [PATCH] Pre-filter saturating sequences only. Retaining singletons
 seems to improve matching accuracy in high sample rate test (well populations
 10% of total cell sample size)

---
 src/main/java/Simulator.java | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index 933ad0e..03bb9e2 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -48,10 +48,10 @@ public class Simulator implements GraphModificationFunctions {
         if(verbose){System.out.println("Well maps made");}
 
 
-//        if(verbose){System.out.println("Removing singleton sequences and sequences present in all wells.");}
-//        filterByOccupancyThresholds(allAlphas, 2, numWells - 1);
-//        filterByOccupancyThresholds(allBetas, 2, numWells - 1);
-//        if(verbose){System.out.println("Sequences removed");}
+        if(verbose){System.out.println("Removing sequences present in all wells.");}
+        filterByOccupancyThresholds(allAlphas, 1, numWells - 1);
+        filterByOccupancyThresholds(allBetas, 1, numWells - 1);
+        if(verbose){System.out.println("Sequences removed");}
         int pairableAlphaCount = allAlphas.size();
         if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);}
         int pairableBetaCount = allBetas.size();