I would like to change the PCR protocol, but the description on the .PAR Simulation Parameters does not provide the details on how to change this. Do I need to use a separate file, or is the protocol encoded in the .PAR file with a specific format? 

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2 Comments

  1. Thasso Griebel

    The Simulator comes with a tool to create different distributions to simulate the PCR. The tool is called pcrdistributions and you can use it by adding the -t option. For example, to get the help:

    ./bin/flux-simulator -t pcrdistributions --help
Create a set of pcr distributions with n generations
Tool specific options:
  (-o|--out) <file>
        Output File
  (-g|--generations) <rounds>
        number of generations (PCR rounds)
  [(-b|--bins) <bins>]
        number of bins (default: 20)
  [--validate <validate>]
        file to validate or 'default'
  [--probability <probability>]
        print distributions for this probability

    This will create a distribution for each generation and store it in the output file. This file can then be referenced from the Simulators's parameter file.

    1. Andrew Tritt

      I tried running that tool, but it looks like it's having a problem parsing the arguments:

      $ ./bin/flux-simulator -t pcrdistributions -o pcr.out -g 10 
/jgi/tools/bin/java
Flux-Simulator v1.2 (Flux Library: 1.19)
[ERROR] Parameter error : java.lang.Integer cannot be cast to java.lang.String
java.lang.ClassCastException: java.lang.Integer cannot be cast to java.lang.String
        at com.martiansoftware.jsap.JSAPResult.getString(Unknown Source)
        at barna.flux.simulator.tools.PCRDistributionsTool.validateParameter(PCRDistributionsTool.java:194)
        at barna.commons.launcher.Flux.main(Flux.java:182)