org.bdgenomics.adam.cli

PrintADAM

class PrintADAM extends ADAMSparkCommand[PrintADAMArgs]

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  1. PrintADAM
  2. ADAMSparkCommand
  3. SparkCommand
  4. ADAMCommand
  5. Runnable
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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
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  6. val args: PrintADAMArgs

    Attributes
    protected
    Definition Classes
    PrintADAMADAMSparkCommand
  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
    PrintADAMADAMCommand
  10. def createSparkContext(args: SparkArgs): SparkContext

    Definition Classes
    SparkCommand
  11. def displayRaw(sc: SparkContext, file: String, pretty: Boolean = false, output: Option[String] = None): Unit

    Display any Parquet file using JSON

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

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

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

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

    Definition Classes
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  16. def hashCode(): Int

    Definition Classes
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  17. final def isInstanceOf[T0]: Boolean

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

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

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

    Definition Classes
    AnyRef
  21. def parseEnvVariables(envVariables: ArrayList[String]): Array[(String, String)]

    Commandline format is -spark_env foo=1 -spark_env bar=2

    Commandline format is -spark_env foo=1 -spark_env bar=2

    envVariables

    The variables found on the commandline

    returns

    Definition Classes
    SparkCommand
  22. def run(sc: SparkContext, job: Job): Unit

    Definition Classes
    PrintADAMADAMSparkCommand
  23. def run(): Unit

    Definition Classes
    ADAMSparkCommand → Runnable
  24. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef
  25. def toString(): String

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

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

    Definition Classes
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    @throws( ... )
  28. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  29. 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.

Inherited from SparkCommand

Inherited from ADAMCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

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