org.bdgenomics.adam.converters

# VariantContextConverter

#### class VariantContextConverter extends Serializable with Logging

This class converts VCF data to and from ADAM. This translation occurs at the abstraction level of the GATK VariantContext which represents VCF data, and at the ADAMVariantContext level, which aggregates ADAM variant/genotype/annotation data together.

If an annotation has a corresponding set of fields in the VCF standard, a conversion to/from the GATK VariantContext should be implemented in this class.

Linear Supertypes
Logging, Serializable, Serializable, AnyRef, Any
Ordering

1. Alphabetic
2. By inheritance

Inherited

1. VariantContextConverter
2. Logging
3. Serializable
4. Serializable
5. AnyRef
6. Any

1. Hide All
2. Show all

Learn more about member selection
Visibility

1. Public
2. All

### Instance Constructors

1. #### new VariantContextConverter(dict: Option[SequenceDictionary] = None)

### 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. #### def convert(vc: VariantContext): VariantContext

   Convert an ADAMVariantContext into the equivalent GATK VariantContext

   Convert an ADAMVariantContext into the equivalent GATK VariantContext

   vc
   returns

     GATK VariantContext

7. #### def convert(vc: VariantContext): Seq[VariantContext]

   Converts a single GATK variant into ADAMVariantContext(s).

   Converts a single GATK variant into ADAMVariantContext(s).

   vc

     GATK Variant context to convert.

   returns

     ADAM variant contexts

8. #### def convertToAnnotation(vc: VariantContext): DatabaseVariantAnnotation

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

   Definition Classes
     AnyRef

10. #### def equals(arg0: Any): Boolean

    Definition Classes
      AnyRef → Any

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

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

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

    Definition Classes
      AnyRef → Any

13. #### def hashCode(): Int

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      Any

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

    Attributes
      protected
    Definition Classes
      Logging

16. #### def jFloat(f: Float): Float

17. #### def log: Logger

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

24. #### def logName: String

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

33. #### def toString(): String

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

36. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from Logging

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped