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 The cell sample file to use -d,--dropout-rate The sequence dropout rate due to amplification error. (0.0 - 1.0) + -exp 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 If using -gaussian flag, standard deviation for distrbution -w,--wells The number of wells on the sample plate + -zipf Use a Zipf distribution for cell sample usage: BiGpairSEQ_Sim.jar -graph -c,--cell-file 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; }