Package org.broadinstitute.hellbender.cmdline.GATKPlugin

Class GATKAnnotationArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationArgumentCollection

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

DefaultGATKVariantAnnotationArgumentCollection

public abstract class GATKAnnotationArgumentCollection
extends Object
implements Serializable

An abstract ArgumentCollection for defining the set of annotation descriptor plugin arguments that are exposed to the user on the command line. Subclasses should provide Argument annotations for the arguments that should be exposed.

See Also:

• GATKAnnotationPluginDescriptor
• Serialized Form

Constructor Summary

Constructors

Constructor	Description
GATKAnnotationArgumentCollection()

Method Summary

Modifier and Type	Method	Description
abstract boolean	getDisableToolDefaultAnnotations()	Returns true if all tool-default annotations are disabled; false otherwise.
abstract boolean	getEnableAllAnnotations()	Returns true if all annotations are enabled; false otherwise.
abstract List<String>	getUserDisabledAnnotationNames()	Returns the disabled annotation names.
abstract List<String>	getUserEnabledAnnotationGroups()	Returns the enabled annotation.
abstract List<String>	getUserEnabledAnnotationNames()	Returns the enabled annotation.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

GATKAnnotationArgumentCollection

public GATKAnnotationArgumentCollection()

Method Details

getUserEnabledAnnotationNames

public abstract List<String> getUserEnabledAnnotationNames()

Returns the enabled annotation. Order should be honored.

getUserEnabledAnnotationGroups

public abstract List<String> getUserEnabledAnnotationGroups()

Returns the enabled annotation. Order should be honored.

getUserDisabledAnnotationNames

public abstract List<String> getUserDisabledAnnotationNames()

Returns the disabled annotation names. Order should be honored.

getDisableToolDefaultAnnotations

public abstract boolean getDisableToolDefaultAnnotations()

Returns true if all tool-default annotations are disabled; false otherwise.

getEnableAllAnnotations

public abstract boolean getEnableAllAnnotations()

Returns true if all annotations are enabled; false otherwise.