Class/Object

org.bdgenomics.adam.cli

ADAM2Vcf

Related Docs: object ADAM2Vcf | package cli

Permalink

class ADAM2Vcf extends BDGSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging

Linear Supertypes
DictionaryCommand, BDGSparkCommand[ADAM2VcfArgs], Logging, BDGCommand, Runnable, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. ADAM2Vcf
  2. DictionaryCommand
  3. BDGSparkCommand
  4. Logging
  5. BDGCommand
  6. Runnable
  7. AnyRef
  8. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

  1. new ADAM2Vcf(args: ADAM2VcfArgs)

    Permalink

Value Members

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

    Permalink
    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  4. val args: ADAM2VcfArgs

    Permalink
    Definition Classes
    ADAM2Vcf → BDGSparkCommand

  5. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any

  6. def clone(): AnyRef

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

  7. val companion: ADAM2Vcf.type

    Permalink
    Definition Classes
    ADAM2Vcf → BDGCommand

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

    Permalink
    Definition Classes
    AnyRef

  9. def equals(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  10. def finalize(): Unit

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

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

    Permalink
    Definition Classes
    AnyRef → Any

  12. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any

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

    Permalink
    Definition Classes
    BDGSparkCommand

  14. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any

  15. def isTraceEnabled(): Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Definition Classes
    DictionaryCommand

  17. def log: Logger

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  24. def logName: String

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Definition Classes
    AnyRef

  30. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef

  31. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef

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

    Permalink
    Definition Classes
    BDGSparkCommand

  33. def run(sc: SparkContext): Unit

    Permalink
    Definition Classes
    ADAM2Vcf → BDGSparkCommand

  34. def run(): Unit

    Permalink
    Definition Classes
    BDGSparkCommand → Runnable

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

    Permalink
    Definition Classes
    AnyRef

  36. def toString(): String

    Permalink
    Definition Classes
    AnyRef → Any

  37. final def wait(): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    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