From 86371668d5ee02f6a4abf9657a03609711be1597 Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Mon, 26 Sep 2022 13:47:19 -0500
Subject: [PATCH] Add menu option to activate simulation of read depth and
 sequence read errors

---
 src/main/java/BiGpairSEQ.java           | 2 +-
 src/main/java/InteractiveInterface.java | 6 ++++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/main/java/BiGpairSEQ.java b/src/main/java/BiGpairSEQ.java
index 9beaea2..45d9622 100644
--- a/src/main/java/BiGpairSEQ.java
+++ b/src/main/java/BiGpairSEQ.java
@@ -176,7 +176,7 @@ public class BiGpairSEQ {
     public static void setOutputGraphML(boolean b) {outputGraphML = b;}
     public static String getVersion() { return version; }
 
-    public static boolean getSimulateReadDepth() {
+    public static boolean simulateReadDepth() {
         return simulateReadDepth;
     }
 
diff --git a/src/main/java/InteractiveInterface.java b/src/main/java/InteractiveInterface.java
index 5055e00..f37d923 100644
--- a/src/main/java/InteractiveInterface.java
+++ b/src/main/java/InteractiveInterface.java
@@ -505,7 +505,8 @@ public class InteractiveInterface {
             System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching");
             System.out.println("4) Turn " + getOnOff(!BiGpairSEQ.outputBinary()) + " serialized binary graph output");
             System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output (for data portability to other programs)");
-            System.out.println("6) Maximum weight matching algorithm options");
+            System.out.println("6) Turn " + getOnOff(!BiGpairSEQ.simulateReadDepth()) + " simulation of read depth and sequence read errors");
+            System.out.println("7) Maximum weight matching algorithm options");
             System.out.println("0) Return to main menu");
             try {
                 input = sc.nextInt();
@@ -515,7 +516,8 @@ public class InteractiveInterface {
                     case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
                     case 4 -> BiGpairSEQ.setOutputBinary(!BiGpairSEQ.outputBinary());
                     case 5 -> BiGpairSEQ.setOutputGraphML(!BiGpairSEQ.outputGraphML());
-                    case 6 -> algorithmOptions();
+                    case 6 -> BiGpairSEQ.setSimulateReadDepth(!BiGpairSEQ.simulateReadDepth());
+                    case 7 -> algorithmOptions();
                     case 0 -> backToMain = true;
                     default -> System.out.println("Invalid input");
                 }