ADAM_2.12: Core 0.30.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package converters
  Definition Classes
    adam
- AlignmentConverter
- DefaultHeaderLines
- VariantContextConverter

c

org.bdgenomics.adam.converters

# VariantContextConverter 

###
Companion object 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
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Inherited

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

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Visibility

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### Instance Constructors

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

### 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
     @native() @throws( ... )
6.  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.

7.  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)

8.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
9.  def equals(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
10.  def finalize(): Unit
    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )
11.  final def getClass(): Class[_]
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      AnyRef → Any
    Annotations
      @native()
12.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
13.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
14.  def isTraceEnabled(): Boolean
    Attributes
      protected
    Definition Classes
      Logging
15.  def log: Logger
    Attributes
      protected
    Definition Classes
      Logging
16.  def logDebug(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
17.  def logDebug(msg: ⇒ String): Unit
    Attributes
      protected
    Definition Classes
      Logging
18.  def logError(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
19.  def logError(msg: ⇒ String): Unit
    Attributes
      protected
    Definition Classes
      Logging
20.  def logInfo(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
21.  def logInfo(msg: ⇒ String): Unit
    Attributes
      protected
    Definition Classes
      Logging
22.  def logName: String
    Attributes
      protected
    Definition Classes
      Logging
23.  def logTrace(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
24.  def logTrace(msg: ⇒ String): Unit
    Attributes
      protected
    Definition Classes
      Logging
25.  def logWarning(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
26.  def logWarning(msg: ⇒ String): Unit
    Attributes
      protected
    Definition Classes
      Logging
27.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
28.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
29.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
30.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
31.  def toString(): String
    Definition Classes
      AnyRef → Any
32.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
33.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
34.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @throws( ... )

### Inherited from Logging

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped