ADAM_2.12: Core 0.32.0 API < Back
 

# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package models
  Definition Classes
    adam
- Alphabet
- Attribute
- Coverage
- DNAAlphabet
- MdTag
- MdTagEvent
- OptionalPositionOrdering
- OptionalReferenceOrdering
- OptionalRegionOrdering
- PositionOrdering
- ReadGroup
- ReadGroupDictionary
- ReferenceOrdering
- ReferencePosition
- ReferencePositionSerializer
- ReferenceRegion
- ReferenceRegionSerializer
- RegionOrdering
- SequenceDictionary
- SequenceRecord
- SnpTable
- Symbol
- TagType
- VariantContext
- VariantContextSerializer

c

org.bdgenomics.adam.models

# VariantContext 

###
Companion object VariantContext

#### class VariantContext extends Serializable

A representation of all variation data at a single variant.

This class represents an equivalent to a single allele from a VCF line, and is the ADAM equivalent to htsjdk.variant.variantcontext.VariantContext.

Linear Supertypes
Serializable, Serializable, AnyRef, Any
 
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. VariantContext
2. Serializable
3. Serializable
4. AnyRef
5. Any

1. Hide All
2. Show All

Visibility

1. Public
2. All

### Instance Constructors

1.  new VariantContext(position: ReferencePosition, variant: RichVariant, genotypes: Iterable[Genotype])

   position

     The locus that the variant is at.

   variant

     The variant allele that is contained in this VariantContext.

   genotypes

     An iterable collection of Genotypes where this allele was called. Equivalent to the per-sample FORMAT fields in a VCF.

### 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.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
7.  def equals(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
8.  def finalize(): Unit
   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] )
9.  val genotypes: Iterable[Genotype]
10.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
11.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
12.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
13.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
14.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
15.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
16.  val position: ReferencePosition
17.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
18.  def toString(): String
    Definition Classes
      AnyRef → Any
19.  val variant: RichVariant
20.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
21.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
22.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @throws( ... )

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped