Class PicardCommandLine

java.lang.Object
picard.cmdline.PicardCommandLine

public class PicardCommandLine extends Object
This is the main class of Picard and is the way of executing individual command line programs. CommandLinePrograms are listed in a single command line interface based on the java package specified to instanceMain. If you want your own single command line program, extend this class and give instanceMain a new list of java packages in which to search for classes that extend CommandLineProgram.
  • Constructor Details

    • PicardCommandLine

      public PicardCommandLine()
  • Method Details

    • getPackageList

      protected static List<String> getPackageList()
      The packages we wish to include in our command line
    • instanceMain

      protected int instanceMain(String[] args, List<String> packageList, String commandLineName)
      The main method. Give a list of java packages in which to search for classes that extend CommandLineProgram. Those will be included on the command line.
    • instanceMain

      protected int instanceMain(String[] args)
      For testing
    • main

      public static void main(String[] args)
      Override this if you want to include different java packages to search for classes that extend CommandLineProgram.
    • processAllCommandLinePrograms

      public static void processAllCommandLinePrograms(List<String> packageList, BiConsumer<Class<CommandLineProgram>,org.broadinstitute.barclay.argparser.CommandLineProgramProperties> clpClassProcessor)
      Process each CommandLineProgram-derived class given a list of packages.
      Parameters:
      packageList - list of packages to search
      clpClassProcessor - function to process each CommandLineProgram class found in packageList (note that the CommandLineProgramProperties argument may be null)
    • getProgramProperty

      public static org.broadinstitute.barclay.argparser.CommandLineProgramProperties getProgramProperty(Class clazz)
    • printUnknown

      public static void printUnknown(Set<Class<?>> classes, String command)
      When a command does not match any known command, searches for similar commands, using the same method as GIT