Class/Object

org.bdgenomics.adam.cli

TransformFragments

Related Docs: object TransformFragments | package cli

Permalink

class TransformFragments extends BDGSparkCommand[TransformFragmentsArgs] with Logging

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

Instance Constructors

  1. new TransformFragments(args: TransformFragmentsArgs)

    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: TransformFragmentsArgs

    Permalink
    Attributes
    protected
    Definition Classes
    TransformFragments → 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: TransformFragments.type

    Permalink
    Definition Classes
    TransformFragments → BDGCommand

  8. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  9. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  10. def debug(msg: ⇒ Any): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Definition Classes
    AnyRef

  12. def equals(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  13. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  14. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  15. def error(msg: ⇒ Any): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  16. def finalize(): Unit

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

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

    Permalink
    Definition Classes
    AnyRef → Any

  18. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  19. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  20. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  21. def info(msg: ⇒ Any): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  22. def isDebugEnabled: Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  23. def isErrorEnabled: Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  24. def isInfoEnabled: Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  25. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any

  26. def isTraceEnabled: Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  27. def isWarnEnabled: Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  28. def logger: Logger

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  29. def loggerName: String

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  30. def maybeDedupe(reads: FragmentDataset): FragmentDataset

    Permalink

    reads

    An RDD of fragments.

    returns

    If the mark duplicates argument is sent, deduplicates the reads. Else, returns the input reads.

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

    Permalink
    Definition Classes
    AnyRef

  32. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef

  33. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef

  34. def run(sc: SparkContext): Unit

    Permalink
    Definition Classes
    TransformFragments → BDGSparkCommand

  35. def run(): Unit

    Permalink
    Definition Classes
    BDGSparkCommand → Runnable

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

    Permalink
    Definition Classes
    AnyRef

  37. def toString(): String

    Permalink
    Definition Classes
    AnyRef → Any

  38. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  39. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  40. def trace(msg: ⇒ Any): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  41. final def wait(): Unit

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

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

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

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

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

  44. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  45. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  46. def warn(msg: ⇒ Any): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

Inherited from BDGSparkCommand[TransformFragmentsArgs]

Inherited from Logging

Inherited from BDGCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

Ungrouped