Class

org.bdgenomics.adam.rdd.variant

VCFOutFormatter

Related Doc: package variant

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case class VCFOutFormatter(conf: Configuration) extends OutFormatter[VariantContext] with Logging with Product with Serializable

OutFormatter that reads streaming VCF.

Linear Supertypes
Product, Equals, Logging, OutFormatter[VariantContext], Serializable, Serializable, AnyRef, Any
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Inherited
  1. VCFOutFormatter
  2. Product
  3. Equals
  4. Logging
  5. OutFormatter
  6. Serializable
  7. Serializable
  8. AnyRef
  9. Any
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Visibility
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Instance Constructors

  1. new VCFOutFormatter(conf: Configuration)

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Value Members

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

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    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  5. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  6. val conf: Configuration

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

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    Definition Classes
    AnyRef
  8. def finalize(): Unit

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

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    Definition Classes
    AnyRef → Any
  10. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  11. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  12. def log: Logger

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    Attributes
    protected
    Definition Classes
    Logging
  13. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  14. def logDebug(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  15. def logError(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  16. def logError(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  17. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  18. def logInfo(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  19. def logName: String

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    Attributes
    protected
    Definition Classes
    Logging
  20. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  21. def logTrace(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  22. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  23. def logWarning(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  24. final def ne(arg0: AnyRef): Boolean

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

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

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    Definition Classes
    AnyRef
  27. def read(is: InputStream): Iterator[VariantContext]

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    Reads VariantContexts from an input stream.

    Reads VariantContexts from an input stream. Autodetects VCF format.

    is

    An InputStream connected to a process we are piping from.

    returns

    Returns an iterator of AlignmentRecords read from the stream.

    Definition Classes
    VCFOutFormatterOutFormatter
  28. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  29. final def wait(): Unit

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  31. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from Logging

Inherited from OutFormatter[VariantContext]

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped