org.bdgenomics.adam.rdd.variant

# VCFOutFormatter

###
Related Doc: package variant

#### case class VCFOutFormatter(conf: Configuration, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]]) extends OutFormatter[VariantContext] with Logging with Product with Serializable

OutFormatter that reads streaming VCF.

conf

  Hadoop configuration.

optHeaderLines

  Optional accumulator for VCF header lines.

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

Visibility

1. Public
2. All

### Instance Constructors

1. #### new VCFOutFormatter(conf: Configuration, acc: CollectionAccumulator[VCFHeaderLine])

   OutFormatter that reads streaming VCF.

   OutFormatter that reads streaming VCF. Java-friendly constructor.

   conf

     Hadoop configuration.

   acc

     Accumulator for VCF header lines.

2. #### new VCFOutFormatter(conf: Configuration)

   OutFormatter that reads streaming VCF.

   OutFormatter that reads streaming VCF. Java-friendly no-arg constructor.

   conf

     Hadoop configuration.

3. #### new VCFOutFormatter(conf: Configuration, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]])

   conf

     Hadoop configuration.

   optHeaderLines

     Optional accumulator for VCF header lines.

### Value Members

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

   Definition Classes
     AnyRef → Any

2. #### final def ##(): Int

   Definition Classes
     AnyRef → Any

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

   Definition Classes
     AnyRef → Any

4. #### final def asInstanceOf[T0]: T0

   Definition Classes
     Any

5. #### def clone(): AnyRef

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

6. #### val conf: Configuration

   Hadoop configuration.

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

   Definition Classes
     AnyRef

8. #### def finalize(): Unit

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

9. #### final def getClass(): Class[_]

   Definition Classes
     AnyRef → Any

10. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

11. #### def isTraceEnabled(): Boolean

    Attributes
      protected
    Definition Classes
      Logging

12. #### def log: Logger

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

14. #### def logDebug(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

16. #### def logError(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

18. #### def logInfo(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

19. #### def logName: String

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

21. #### def logTrace(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

23. #### def logWarning(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

24. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

25. #### final def notify(): Unit

    Definition Classes
      AnyRef

26. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

27. #### val optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]]

    Optional accumulator for VCF header lines.

28. #### 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

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

    Definition Classes
      AnyRef

30. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

32. #### 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 AnyRef

### Inherited from Any

### Ungrouped