From 077af3b46ede0a61ea046006b8678866bdaaf1f7 Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Mon, 26 Sep 2022 23:17:10 -0500
Subject: [PATCH] Clear plate in memory when simulating read depth

---
 src/main/java/InteractiveInterface.java | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/main/java/InteractiveInterface.java b/src/main/java/InteractiveInterface.java
index 25304c4..45c307a 100644
--- a/src/main/java/InteractiveInterface.java
+++ b/src/main/java/InteractiveInterface.java
@@ -264,6 +264,7 @@ public class InteractiveInterface {
             System.out.print("\nPlease enter name of an existing sample plate file: ");
             plateFile = sc.next();
             System.out.println("\nEnable simulation of sequence read depth and sequence read errors? (y/n)");
+            System.out.println("NOTE: sample plate data cannot be cached when simulating read errors");
             String ans = sc.next();
             Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
             Matcher matcher = pattern.matcher(ans);
@@ -271,6 +272,8 @@ public class InteractiveInterface {
                 simulateReadDepth = true;
             }
             if (simulateReadDepth) {
+                BiGpairSEQ.setCachePlate(false);
+                BiGpairSEQ.clearPlateInMemory();
                 System.out.print("\nPlease enter read depth (the integer number of reads per sequence): ");
                 readDepth = sc.nextInt();
                 if(readDepth < 1) {