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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  1. 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. 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 
      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)