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 a user tries to run the tool, the helpful message in the tool's registry entry will be issued.