From 22faad34145e0eeffcfa59e21b17b8d238ea4d5d Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Wed, 28 Sep 2022 17:45:09 -0500
Subject: [PATCH] Add real sequence collision rate

---
 src/main/java/Simulator.java | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index 08efcf6..ab4f27a 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -27,7 +27,8 @@ public class Simulator implements GraphModificationFunctions {
 
 
     public static GraphWithMapData makeCDR3Graph(CellSample cellSample, Plate samplePlate, int readDepth,
-                                                 double readErrorRate, double errorCollisionRate, boolean verbose) {
+                                                 double readErrorRate, double errorCollisionRate,
+                                                 double realSequenceCollisionRate, boolean verbose) {
         //start timing
         Instant start = Instant.now();
         int[] alphaIndices = {SequenceType.CDR3_ALPHA.ordinal()};
@@ -44,11 +45,11 @@ public class Simulator implements GraphModificationFunctions {
         //Make linkedHashMap keyed to sequences, values are SequenceRecords reflecting plate statistics
         if(verbose){System.out.println("Making sample plate sequence maps");}
         Map<String, SequenceRecord> alphaSequences = samplePlate.countSequences(readDepth, readErrorRate,
-                errorCollisionRate, alphaIndices);
+                errorCollisionRate, realSequenceCollisionRate, alphaIndices);
         int alphaCount = alphaSequences.size();
         if(verbose){System.out.println("Alphas sequences read: " + alphaCount);}
         Map<String, SequenceRecord> betaSequences = samplePlate.countSequences(readDepth, readErrorRate,
-                errorCollisionRate, betaIndices);
+                errorCollisionRate, realSequenceCollisionRate, betaIndices);
         int betaCount = betaSequences.size();
         if(verbose){System.out.println("Betas sequences read: " + betaCount);}
         if(verbose){System.out.println("Sample plate sequence maps made");}
@@ -131,7 +132,7 @@ 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, time);
+                alphaCount, betaCount, readDepth, readErrorRate, errorCollisionRate, realSequenceCollisionRate, time);
         //Set source file name in graph to name of sample plate
         output.setSourceFilename(samplePlate.getFilename());
         //return GraphWithMapData object
@@ -307,6 +308,7 @@ public class Simulator implements GraphModificationFunctions {
         metadata.put("sequence 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("real sequence collision rate", data.getRealSequenceCollisionRate().toString());
         metadata.put("total alphas read from plate", data.getAlphaCount().toString());
         metadata.put("total betas read from plate", data.getBetaCount().toString());
         //HARD CODED, PARAMETERIZE LATER