org.bdgenomics.adam.apis.java

JavaADAMPluginWithoutPredicate

abstract class JavaADAMPluginWithoutPredicate[Input, Output] extends JavaADAMPlugin[Input, Output]

Plugins that do not want to apply a predicate should extend this class.

Linear Supertypes
JavaADAMPlugin[Input, Output], Serializable, Serializable, ADAMPlugin[Input, Output], AnyRef, Any
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Inherited
  1. JavaADAMPluginWithoutPredicate
  2. JavaADAMPlugin
  3. Serializable
  4. Serializable
  5. ADAMPlugin
  6. AnyRef
  7. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new JavaADAMPluginWithoutPredicate()

Abstract Value Members

  1. abstract def recordProjection: Schema

    The fields of the input record that should be populated.

    The fields of the input record that should be populated. If a projection should not be applied, this should be null. Code upstream will check for a null value, so this is safe.

    returns

    A schema describing the projection to apply to all records.

    Definition Classes
    JavaADAMPlugin
  2. abstract def run(jsc: JavaSparkContext, recs: JavaRDD[Input], args: String): JavaRDD[Output]

    Run method to be implemented by plugin implementor.

    Run method to be implemented by plugin implementor.

    jsc

    Java Spark Context that this plugin is running inside of.

    recs

    Input RDD of records.

    args

    Command line arguments passed to this plugin.

    returns

    Output RDD to be saved to disk.

    Definition Classes
    JavaADAMPlugin

Concrete Value Members

  1. final def !=(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0

    Definition Classes
    Any
  5. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  6. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  7. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any
  8. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  9. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any
  10. def hashCode(): Int

    Definition Classes
    AnyRef → Any
  11. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  12. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  13. final def notify(): Unit

    Definition Classes
    AnyRef
  14. final def notifyAll(): Unit

    Definition Classes
    AnyRef
  15. final def predicate: Option[(Input) ⇒ Boolean]

    Definition Classes
    JavaADAMPluginWithoutPredicate → ADAMPlugin
  16. final def projection: Option[Schema]

    Definition Classes
    JavaADAMPlugin → ADAMPlugin
  17. final def run(sc: SparkContext, recs: RDD[Input], args: String): RDD[Output]

    Definition Classes
    JavaADAMPlugin → ADAMPlugin
  18. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef
  19. def toString(): String

    Definition Classes
    AnyRef → Any
  20. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  21. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  22. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from JavaADAMPlugin[Input, Output]

Inherited from Serializable

Inherited from Serializable

Inherited from ADAMPlugin[Input, Output]

Inherited from AnyRef

Inherited from Any

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