ADAM_2.12: Core 0.36.0 API < Back
 

# 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
 
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)

### 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[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native() @HotSpotIntrinsicCandidate()
6.  def convert(vc: VariantContext): Option[VariantContext]

   Convert an ADAM variant context into a htsjdk variant context.

   Convert an ADAM variant context into a htsjdk variant context.

   vc

     ADAM variant context to convert.

   returns

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

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

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

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

   vc

     htsjdk variant context to convert.

   returns

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

8.  def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
   Attributes
     protected
   Definition Classes
     Logging
9.  def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
   Attributes
     protected
   Definition Classes
     Logging
10.  def debug(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
11.  final def eq(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
12.  def equals(arg0: Any): Boolean
    Definition Classes
      AnyRef → Any
13.  def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
14.  def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
15.  def error(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
16.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
17.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
18.  def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
19.  def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
20.  def info(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
21.  def isDebugEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
22.  def isErrorEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
23.  def isInfoEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
24.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
25.  def isTraceEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
26.  def isWarnEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
27.  def logger: Logger
    Attributes
      protected
    Definition Classes
      Logging
28.  def loggerName: String
    Attributes
      protected
    Definition Classes
      Logging
29.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
30.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
31.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
32.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
33.  def toString(): String
    Definition Classes
      AnyRef → Any
34.  def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
35.  def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
36.  def trace(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
37.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
38.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
39.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
40.  def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
41.  def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
42.  def warn(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging

### Deprecated Value Members

1.  def finalize(): Unit
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
   Deprecated

     (Since version ) see corresponding Javadoc for more information.

### Inherited from Logging

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped