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 htsjdk VariantContext which represents VCF data, and at the ADAMVariantContext level, which aggregates ADAM variant/genotype/annotation data together.

If a genotype annotation has a corresponding set of fields in the VCF standard, a conversion to/from the htsjdk 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(headerLines: Seq[VCFHeaderLine], stringency: ValidationStringency)

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. def convert(vc: VariantContext): Option[VariantContext]

    Convert an ADAM variant context into a GATK variant context.

    Convert an ADAM variant context into a GATK variant context.

    vc

    ADAM variant context to convert.

    returns

    The specified ADAM variant context converted into a GATK variant context.

  9. def convert(vc: VariantContext): Seq[VariantContext]

    Converts a GATK variant context into one or more ADAM variant context(s).

    Converts a GATK variant context into one or more ADAM variant context(s).

    vc

    GATK variant context to convert.

    returns

    The specified GATK variant context converted into one or more ADAM variant context(s)

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

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

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

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

    Definition Classes
    AnyRef → Any
  14. def hashCode(): Int

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

    Definition Classes
    Any
  16. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging
  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 Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped