# Package picard.cmdline

- Interface Summary
  Interface | Description
  --- | ---
  CommandLineParser.ClpEnum |
  CommandLineProgramGroup | Interface for groups of CommandLinePrograms.

- Class Summary
  Class | Description
  --- | ---
  ClassFinder | Utility class that can scan for classes in the classpath and find all the ones annotated with a particular annotation.
  CommandLineDefaults | Embodies defaults for global values that affect how the Picard Command Line operates.
  CommandLineParser | Annotation-driven utility for parsing command-line arguments, checking for errors, and producing usage message.
  CommandLineParser.OptionDefinition |
  CommandLineParser.OptionDefinitionByPrintOrderComparator |
  CommandLineProgram | Abstract class to facilitate writing command-line programs.
  CreateHtmlDocForProgram | Print out the usage for one or more CommandLinePrograms in a form close to what is used in the Sourceforge Picard website.
  CreateHtmlDocForStandardOptions |
  PicardCommandLine | This is the main class of Picard and is the way of executing individual command line programs.
  StandardOptionDefinitions | A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.

- Exception Summary
  Exception | Description
  --- | ---
  CommandLineParseException |
  CommandLineParserDefinitionException |

- Annotation Types Summary
  Annotation Type | Description
  --- | ---
  CommandLineProgramProperties | Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
  NestedOptions | Used to annotate a field in a CommandLineProgram that holds a instance containing @Option-annotated fields.
  Option | Used to annotate which fields of a CommandLineProgram are options given at the command line.
  PositionalArguments | Used to annotate which field of a CommandLineProgram should store parameters given at the command line which are not options.