From b8aeeb988f69afb06a8ec59c8b204c546f8af92f Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Fri, 30 Sep 2022 00:33:41 -0500
Subject: [PATCH] Add sequence dropout rate to metadata output

---
 src/main/java/GraphWithMapData.java | 6 +++++-
 src/main/java/Simulator.java        | 3 ++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/main/java/GraphWithMapData.java b/src/main/java/GraphWithMapData.java
index 4f186dc..d9720b1 100644
--- a/src/main/java/GraphWithMapData.java
+++ b/src/main/java/GraphWithMapData.java
@@ -15,6 +15,7 @@ public class GraphWithMapData implements java.io.Serializable {
     private final Integer[] wellPopulations;
     private final int alphaCount;
     private final int betaCount;
+    private final double dropoutRate;
     private final int readDepth;
     private final double readErrorRate;
     private final double errorCollisionRate;
@@ -30,7 +31,7 @@ public class GraphWithMapData implements java.io.Serializable {
 
     public GraphWithMapData(SimpleWeightedGraph graph, Integer numWells, Integer[] wellConcentrations,
                             Map<String, String> distCellsMapAlphaKey, Integer alphaCount, Integer betaCount,
-                            Integer readDepth, Double readErrorRate, Double errorCollisionRate,
+                            Double dropoutRate, Integer readDepth, Double readErrorRate, Double errorCollisionRate,
                             Double realSequenceCollisionRate, Duration time){
 
 //                            Map<Integer, Integer> plateVtoAMap,
@@ -49,6 +50,7 @@ public class GraphWithMapData implements java.io.Serializable {
 //        this.plateBtoVMap = plateBtoVMap;
 //        this.alphaWellCounts = alphaWellCounts;
 //        this.betaWellCounts = betaWellCounts;
+        this.dropoutRate = dropoutRate;
         this.readDepth = readDepth;
         this.readErrorRate = readErrorRate;
         this.errorCollisionRate = errorCollisionRate;
@@ -127,4 +129,6 @@ public class GraphWithMapData implements java.io.Serializable {
     }
 
     public Double getRealSequenceCollisionRate() { return realSequenceCollisionRate; }
+
+    public Double getDropoutRate() { return dropoutRate; }
 }
diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index a4184ea..2fd5c64 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -136,7 +136,7 @@ public class Simulator implements GraphModificationFunctions {
         Duration time = Duration.between(start, stop);
         //create GraphWithMapData object
         GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), distCellsMapAlphaKey,
-                alphaCount, betaCount, readDepth, readErrorRate, errorCollisionRate, realSequenceCollisionRate, time);
+                alphaCount, betaCount, samplePlate.getError(), readDepth, readErrorRate, errorCollisionRate, realSequenceCollisionRate, time);
         //Set source file name in graph to name of sample plate
         output.setSourceFilename(samplePlate.getFilename());
         //return GraphWithMapData object
@@ -305,6 +305,7 @@ public class Simulator implements GraphModificationFunctions {
 
         Map<String, String> metadata = new LinkedHashMap<>();
         metadata.put("sample plate filename", data.getSourceFilename());
+        metadata.put("sequence dropout rate", data.getDropoutRate().toString());
         metadata.put("graph filename", dataFilename);
         metadata.put("MWM algorithm type", algoType);
         metadata.put("matching weight", totalMatchingWeight.toString());