From 34dc2a5721ab6db5e77adb4db94a505bb0badc3c Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Wed, 28 Sep 2022 17:54:55 -0500
Subject: [PATCH] Add real sequence collision rate

---
 src/main/java/CommandLineInterface.java | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/src/main/java/CommandLineInterface.java b/src/main/java/CommandLineInterface.java
index 9b7580b..5040a8c 100644
--- a/src/main/java/CommandLineInterface.java
+++ b/src/main/java/CommandLineInterface.java
@@ -150,16 +150,21 @@ public class CommandLineInterface {
                 Integer readDepth = 1;
                 Double readErrorRate = 0.0;
                 Double errorCollisionRate = 0.0;
+                Double realSequenceCollisionRate = 0.0;
                 if (line.hasOption("rd")) {
                     readDepth = Integer.parseInt(line.getOptionValue("rd"));
                 }
                 if (line.hasOption("err")) {
                     readErrorRate = Double.parseDouble(line.getOptionValue("err"));
                 }
-                if (line.hasOption("coll")) {
-                    errorCollisionRate = Double.parseDouble(line.getOptionValue("coll"));
+                if (line.hasOption("errcoll")) {
+                    errorCollisionRate = Double.parseDouble(line.getOptionValue("errcoll"));
                 }
-                graph = Simulator.makeCDR3Graph(cells, plate, readDepth, readErrorRate, errorCollisionRate, false);
+                if (line.hasOption("realcoll")) {
+                    realSequenceCollisionRate = Double.parseDouble(line.getOptionValue("realcoll"));
+                }
+                graph = Simulator.makeCDR3Graph(cells, plate, readDepth, readErrorRate, errorCollisionRate,
+                        realSequenceCollisionRate, false);
                 if (!line.hasOption("no-binary")) { //output binary file unless told not to
                     GraphDataObjectWriter writer = new GraphDataObjectWriter(outputFilename, graph, false);
                     writer.writeDataToFile();
@@ -413,12 +418,20 @@ public class CommandLineInterface {
                 .hasArg()
                 .argName("prob")
                 .build();
-        Option errorCollisionProb = Option.builder("coll")
+        Option errorCollisionProb = Option.builder("errcoll")
                 .longOpt("error-collision-prob")
                 .desc("(Optional) The probability that two misreads will produce the same spurious sequence. (0.0 - 1.0)")
                 .hasArg()
                 .argName("prob")
                 .build();
+        Option realSequenceCollisionProb = Option.builder("realcoll")
+                .longOpt("real-collision-prob")
+                .desc("(Optional) The probability that a sequence will be misread " +
+                        "as another real sequence. (Only applies to unique misreads; after this has happened once, " +
+                        "future error collisions could produce the real sequence again) (0.0 - 1.0)")
+                .hasArg()
+                .argName("prob")
+                .build();
         graphOptions.addOption(cellFilename);
         graphOptions.addOption(plateFilename);
         graphOptions.addOption(outputFileOption());
@@ -427,6 +440,7 @@ public class CommandLineInterface {
         graphOptions.addOption(readDepth);
         graphOptions.addOption(readErrorProb);
         graphOptions.addOption(errorCollisionProb);
+        graphOptions.addOption(realSequenceCollisionProb);
         return graphOptions;
     }