From b7597cff2af4c7603d7a592fbe52953a98d5a80b Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Wed, 9 Apr 2025 16:16:46 -0500
Subject: [PATCH] update readme and add Zipf exponent option to CLI

---
 readme.md                               | 6 ++++--
 src/main/java/CommandLineInterface.java | 1 +
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/readme.md b/readme.md
index 8d05e71..d7731d7 100644
--- a/readme.md
+++ b/readme.md
@@ -136,7 +136,7 @@ There are a number of command line options, to allow the program to be used in s
 `java -jar BiGpairSEQ_Sim.jar -help`
 
 ```
-usage: BiGpairSEQ_Sim.jar
+ usage: BiGpairSEQ_Sim.jar
  -cells,--make-cells   Makes a cell sample file of distinct T cells
  -graph,--make-graph   Makes a graph/data file. Requires a cell sample
                        file and a sample plate file
@@ -156,6 +156,8 @@ usage: BiGpairSEQ_Sim.jar -plate
  -c,--cell-file <filename>     The cell sample file to use
  -d,--dropout-rate <rate>      The sequence dropout rate due to
                                amplification error. (0.0 - 1.0)
+ -exp <value>                  If using -zipf flag, exponent value for
+                               distribution
  -exponential                  Use an exponential distribution for cell
                                sample
  -gaussian                     Use a Gaussian distribution for cell sample
@@ -173,6 +175,7 @@ usage: BiGpairSEQ_Sim.jar -plate
  -stddev <value>               If using -gaussian flag, standard deviation
                                for distrbution
  -w,--wells <number>           The number of wells on the sample plate
+ -zipf                         Use a Zipf distribution for cell sample
 
 usage: BiGpairSEQ_Sim.jar -graph
  -c,--cell-file <filename>                Cell sample file to use for
@@ -234,7 +237,6 @@ usage: BiGpairSEQ_Sim.jar -match
                                to stdout.
  -pv,--p-value                 (Optional) Calculate p-values for sequence
                                pairs.
-
 ```
 
 ### INTERACTIVE INTERFACE
diff --git a/src/main/java/CommandLineInterface.java b/src/main/java/CommandLineInterface.java
index 18a3fbe..1f8553c 100644
--- a/src/main/java/CommandLineInterface.java
+++ b/src/main/java/CommandLineInterface.java
@@ -399,6 +399,7 @@ public class CommandLineInterface {
         plateOptions.addOptionGroup(statParams);
         plateOptions.addOptionGroup(wellPopOptions);
         plateOptions.addOption(dropoutRate);
+        plateOptions.addOption(zipfExponent);
         plateOptions.addOption(outputFileOption());
         return plateOptions;
     }