org.bdgenomics.adam.rdd.variant

VCFOutFormatter

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
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. VCFOutFormatter
  2. Product
  3. Equals
  4. Logging
  5. OutFormatter
  6. Serializable
  7. Serializable
  8. AnyRef
  9. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Instance Constructors

  1. new VCFOutFormatter(conf: Configuration)

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
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def clone(): AnyRef

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

  8. val conf: Configuration

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

    Definition Classes
    AnyRef

  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. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  13. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging

  14. def log: Logger

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

  21. def logName: String

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Definition Classes
    AnyRef

  27. final def notify(): Unit

    Definition Classes
    AnyRef

  28. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  29. def read(is: InputStream): Iterator[VariantContext]

    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
    VCFOutFormatter → OutFormatter

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

    Definition Classes
    AnyRef

  31. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    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