From 810abdb705c9175f91e6fef7524b56404dfba7d6 Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Tue, 27 Sep 2022 11:13:12 -0500
Subject: [PATCH] Add read depth parameters to output metadata

---
 src/main/java/GraphWithMapData.java | 18 ++++++++++++++++--
 src/main/java/Simulator.java        | 20 +++++++++++++-------
 2 files changed, 29 insertions(+), 9 deletions(-)

diff --git a/src/main/java/GraphWithMapData.java b/src/main/java/GraphWithMapData.java
index 2d30519..bfa1e19 100644
--- a/src/main/java/GraphWithMapData.java
+++ b/src/main/java/GraphWithMapData.java
@@ -16,6 +16,8 @@ public class GraphWithMapData implements java.io.Serializable {
     private Integer alphaCount;
     private Integer betaCount;
     private int readDepth;
+    private double readErrorRate;
+    private double errorCollisionRate;
     private final Map<String, String> distCellsMapAlphaKey;
 //    private final Map<Integer, Integer> plateVtoAMap;
 //    private final Map<Integer, Integer> plateVtoBMap;
@@ -26,7 +28,8 @@ public class GraphWithMapData implements java.io.Serializable {
     private final Duration time;
 
     public GraphWithMapData(SimpleWeightedGraph graph, Integer numWells, Integer[] wellConcentrations,
-                            Map<String, String> distCellsMapAlphaKey, Integer alphaCount, Integer betaCount, int readDepth, Duration time){
+                            Map<String, String> distCellsMapAlphaKey, Integer alphaCount, Integer betaCount,
+                            Integer readDepth, Double readErrorRate, Double errorCollisionRate, Duration time){
 
 //                            Map<Integer, Integer> plateVtoAMap,
 //                            Map<Integer,Integer> plateVtoBMap, Map<Integer, Integer> plateAtoVMap,
@@ -44,6 +47,9 @@ public class GraphWithMapData implements java.io.Serializable {
 //        this.plateBtoVMap = plateBtoVMap;
 //        this.alphaWellCounts = alphaWellCounts;
 //        this.betaWellCounts = betaWellCounts;
+        this.readDepth = readDepth;
+        this.readErrorRate = readErrorRate;
+        this.errorCollisionRate = errorCollisionRate;
         this.time = time;
     }
 
@@ -95,7 +101,7 @@ public class GraphWithMapData implements java.io.Serializable {
 //        return betaWellCounts;
 //    }
 
-    public int getReadDepth() { return readDepth; }
+    public Integer getReadDepth() { return readDepth; }
 
     public Duration getTime() {
         return time;
@@ -108,4 +114,12 @@ public class GraphWithMapData implements java.io.Serializable {
     public String getSourceFilename() {
         return sourceFilename;
     }
+
+    public Double getReadErrorRate() {
+        return readErrorRate;
+    }
+
+    public Double getErrorCollisionRate() {
+        return errorCollisionRate;
+    }
 }
diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index 4ce0a06..cc24b18 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -168,7 +168,8 @@ 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, time);
+        GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), distCellsMapAlphaKey,
+                alphaCount, betaCount, readDepth, readErrorRate, errorCollisionRate, time);
         //Set source file name in graph to name of sample plate
         output.setSourceFilename(samplePlate.getFilename());
         //return GraphWithMapData object
@@ -340,14 +341,19 @@ public class Simulator implements GraphModificationFunctions {
         metadata.put("algorithm type", algoType);
         metadata.put("matching weight", totalMatchingWeight.toString());
         metadata.put("well populations", wellPopulationsString);
-        metadata.put("total alphas on plate", data.getAlphaCount().toString());
-        metadata.put("total betas on plate", data.getBetaCount().toString());
+        metadata.put("read depth", data.getReadDepth().toString());
+        metadata.put("Sequence read error rate", data.getReadErrorRate().toString());
+        metadata.put("Read error collision rate", data.getErrorCollisionRate().toString());
+        metadata.put("total alphas read from plate", data.getAlphaCount().toString());
+        metadata.put("total betas read from plate", data.getBetaCount().toString());
+        metadata.put("pre-filter sequences present in all wells", "true");
+        metadata.put("pre-filter sequences based on occupancy/read count discrepancy", "true");
         metadata.put("alphas in graph (after pre-filtering)", graphAlphaCount.toString());
         metadata.put("betas in graph (after pre-filtering)", graphBetaCount.toString());
-        metadata.put("high overlap threshold", highThreshold.toString());
-        metadata.put("low overlap threshold", lowThreshold.toString());
-        metadata.put("minimum overlap percent", minOverlapPercent.toString());
-        metadata.put("maximum occupancy difference", maxOccupancyDifference.toString());
+        metadata.put("high overlap threshold for pairing", highThreshold.toString());
+        metadata.put("low overlap threshold for pairing", lowThreshold.toString());
+        metadata.put("minimum overlap percent for pairing", minOverlapPercent.toString());
+        metadata.put("maximum occupancy difference for pairing", maxOccupancyDifference.toString());
         metadata.put("pairing attempt rate", attemptRateTrunc.toString());
         metadata.put("correct pairing count", Integer.toString(trueCount));
         metadata.put("incorrect pairing count", Integer.toString(falseCount));