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update readme and add Zipf exponent option to CLI

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eugenefischer
2025-04-09 16:16:46 -05:00
parent 7bbeaf7dad
commit b7597cff2a
2 changed files with 5 additions and 2 deletions
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6
readme.md
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@@ -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` `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 -cells,--make-cells Makes a cell sample file of distinct T cells
-graph,--make-graph Makes a graph/data file. Requires a cell sample -graph,--make-graph Makes a graph/data file. Requires a cell sample
file and a sample plate file 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 -c,--cell-file <filename> The cell sample file to use
-d,--dropout-rate <rate> The sequence dropout rate due to -d,--dropout-rate <rate> The sequence dropout rate due to
amplification error. (0.0 - 1.0) amplification error. (0.0 - 1.0)
-exp <value> If using -zipf flag, exponent value for
distribution
-exponential Use an exponential distribution for cell -exponential Use an exponential distribution for cell
sample sample
-gaussian Use a Gaussian 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 -stddev <value> If using -gaussian flag, standard deviation
for distrbution for distrbution
-w,--wells <number> The number of wells on the sample plate -w,--wells <number> The number of wells on the sample plate
-zipf Use a Zipf distribution for cell sample
usage: BiGpairSEQ_Sim.jar -graph usage: BiGpairSEQ_Sim.jar -graph
-c,--cell-file <filename> Cell sample file to use for -c,--cell-file <filename> Cell sample file to use for
@@ -234,7 +237,6 @@ usage: BiGpairSEQ_Sim.jar -match
to stdout. to stdout.
-pv,--p-value (Optional) Calculate p-values for sequence -pv,--p-value (Optional) Calculate p-values for sequence
pairs. pairs.
``` ```
### INTERACTIVE INTERFACE ### INTERACTIVE INTERFACE

1
src/main/java/CommandLineInterface.java
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@@ -399,6 +399,7 @@ public class CommandLineInterface {
plateOptions.addOptionGroup(statParams); plateOptions.addOptionGroup(statParams);
plateOptions.addOptionGroup(wellPopOptions); plateOptions.addOptionGroup(wellPopOptions);
plateOptions.addOption(dropoutRate); plateOptions.addOption(dropoutRate);
plateOptions.addOption(zipfExponent);
plateOptions.addOption(outputFileOption()); plateOptions.addOption(outputFileOption());
return plateOptions; return plateOptions;
} }