Deprecating GATK Features

To deprecate any feature that is documented (any @Argument, or any other feature that is annotated with @DocumentedFeature, such as a tool, read filter, or metric), add an @DeprecatedFeature annotation. The @DeprecatedFeature annotation allows an optional detail string that can include any explanation or comforting words of advice for the user:

@DeprecatedFeature(detail="New qual score is on by default") @Argument(fullName = "use-new-qual-calculator", shortName = "new-qual", doc = "Use the new AF model instead of the so-called exact model", optional = true)

The feature will be marked in the online doc and command line help as deprecated. @DeprecatedFeature, @BetaFeature and @ExperimentalFeature are all mutually exclusive.

When the tool is actually removed, it can be added to the DeprecatedToolsRegistry. When the user tries to run the tool, the helpful message in the tool's registry entry will be issued.