Class/Object

org.bdgenomics.adam.converters

VariantContextConverter

Related Docs: object VariantContextConverter | package converters

Permalink

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
Visibility
  1. Public
  2. All

Instance Constructors

  1. new VariantContextConverter(headerLines: Seq[VCFHeaderLine], stringency: ValidationStringency, setNestedAnnotationInGenotype: Boolean)

    Permalink

Value Members

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

    Permalink
    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Permalink
    Definition Classes
    AnyRef → Any

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

    Permalink
    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any

  5. def clone(): AnyRef

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

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

    Permalink

    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.

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

    Permalink

    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)

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

    Permalink
    Definition Classes
    AnyRef

  9. def equals(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  10. def finalize(): Unit

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

  11. final def getClass(): Class[_]

    Permalink
    Definition Classes
    AnyRef → Any

  12. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  13. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any

  14. def isTraceEnabled(): Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  15. def log: Logger

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

  22. def logName: String

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Attributes
    protected
    Definition Classes
    Logging

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

    Permalink
    Definition Classes
    AnyRef

  28. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef

  29. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef

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

    Permalink
    Definition Classes
    AnyRef

  31. def toString(): String

    Permalink
    Definition Classes
    AnyRef → Any

  32. final def wait(): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped