Constructor Detail

• PicardCommandLine

  public PicardCommandLine()

Method Detail

• 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