org.bdgenomics.adam.cli

# PrintADAM

#### class PrintADAM extends ADAMSparkCommand[PrintADAMArgs]

Linear Supertypes
ADAMSparkCommand[PrintADAMArgs], Logging, ADAMCommand, Runnable, AnyRef, Any
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Inherited

1. PrintADAM
2. ADAMSparkCommand
3. Logging
4. ADAMCommand
5. Runnable
6. AnyRef
7. Any

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### Instance Constructors

1. #### new PrintADAM(args: PrintADAMArgs)

### Value Members

1. #### final def !=(arg0: AnyRef): Boolean

   Definition Classes
     AnyRef

2. #### final def !=(arg0: Any): Boolean

   Definition Classes
     Any

3. #### final def ##(): Int

   Definition Classes
     AnyRef → Any

4. #### final def ==(arg0: AnyRef): Boolean

   Definition Classes
     AnyRef

5. #### final def ==(arg0: Any): Boolean

   Definition Classes
     Any

6. #### val args: PrintADAMArgs

   Attributes
     protected
   Definition Classes
     PrintADAM → ADAMSparkCommand

7. #### final def asInstanceOf[T0]: T0

   Definition Classes
     Any

8. #### def clone(): AnyRef

   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... )

9. #### val companion: PrintADAM.type

   Definition Classes
     PrintADAM → ADAMCommand

10. #### def displayRaw(sc: SparkContext, file: String, pretty: Boolean = false, output: Option[String] = None): Unit

    Display any Parquet file using JSON

11. #### final def eq(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

12. #### def equals(arg0: Any): Boolean

    Definition Classes
      AnyRef → Any

13. #### def finalize(): Unit

    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )

14. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

15. #### def hashCode(): Int

    Definition Classes
      AnyRef → Any

16. #### def initializeMetrics(sc: SparkContext): Option[MetricsListener]

    Definition Classes
      ADAMSparkCommand

17. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

18. #### def isTraceEnabled(): Boolean

    Attributes
      protected
    Definition Classes
      Logging

19. #### def log: Logger

    Attributes
      protected
    Definition Classes
      Logging

20. #### def logDebug(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

21. #### def logDebug(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

22. #### def logError(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

23. #### def logError(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

24. #### def logInfo(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

25. #### def logInfo(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

26. #### def logName: String

    Attributes
      protected
    Definition Classes
      Logging

27. #### def logTrace(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

28. #### def logTrace(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

29. #### def logWarning(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

30. #### def logWarning(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

31. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

32. #### final def notify(): Unit

    Definition Classes
      AnyRef

33. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

34. #### def printMetrics(totalTime: Long, metricsListener: Option[MetricsListener]): Unit

    Definition Classes
      ADAMSparkCommand

35. #### def run(sc: SparkContext, job: Job): Unit

    Definition Classes
      PrintADAM → ADAMSparkCommand

36. #### def run(): Unit

    Definition Classes
      ADAMSparkCommand → Runnable

37. #### final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
      AnyRef

38. #### def toString(): String

    Definition Classes
      AnyRef → Any

39. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

40. #### final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

41. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

42. #### def withPrintStream(filename: Option[String])(op: (PrintStream) ⇒ Unit): Unit

    Safe output-stream “resource” function

    Safe output-stream “resource” function

    This function calls the function op on a java.io.PrintStream, if filename is None, it uses System.out. If the function ends with an exception, and filename is Some(_), the output stream will be closed.

    filename

      If provided, this is the output to print to. Else, if None, we print to System.out.

### Inherited from ADAMSparkCommand[PrintADAMArgs]

### Inherited from Logging

### Inherited from ADAMCommand

### Inherited from Runnable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped