From 4f2fa4cbbef35e6623f3f4e00fb3fafdc27e5353 Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Sun, 25 Sep 2022 15:19:56 -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 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index 5deac67..c844d88 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -48,9 +48,9 @@ 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("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);}