org.bdgenomics.adam.cli

# ADAM2Vcf

#### class ADAM2Vcf extends BDGSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging

Linear Supertypes
DictionaryCommand, BDGSparkCommand[ADAM2VcfArgs], Logging, BDGCommand, Runnable, AnyRef, Any
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Inherited

1. ADAM2Vcf
2. DictionaryCommand
3. BDGSparkCommand
4. Logging
5. BDGCommand
6. Runnable
7. AnyRef
8. Any

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### Instance Constructors

1. #### new ADAM2Vcf(args: ADAM2VcfArgs)

### 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. #### val args: ADAM2VcfArgs

   Definition Classes
     ADAM2Vcf → BDGSparkCommand

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

   Definition Classes
     Any

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

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

7. #### val companion: ADAM2Vcf.type

   Definition Classes
     ADAM2Vcf → BDGCommand

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

   Definition Classes
     AnyRef

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

   Definition Classes
     AnyRef → Any

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

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

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      BDGSparkCommand

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

    Definition Classes
      Any

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

    Attributes
      protected
    Definition Classes
      Logging

16. #### def loadSequenceDictionary(file: File): Option[SequenceDictionary]

    Definition Classes
      DictionaryCommand

17. #### def log: Logger

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

24. #### def logName: String

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      BDGSparkCommand

33. #### def run(sc: SparkContext): Unit

    Definition Classes
      ADAM2Vcf → BDGSparkCommand

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

    Definition Classes
      BDGSparkCommand → Runnable

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from DictionaryCommand

### Inherited from BDGSparkCommand[ADAM2VcfArgs]

### Inherited from Logging

### Inherited from BDGCommand

### Inherited from Runnable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped