ADAM_2.12: Core 1.0.1 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 sql
  Definition Classes
    adam
- Alignment
- Dbxref
- Feature
- Fragment
- Genotype
- OntologyTerm
- ProcessingStep
- Read
- Reference
- Sequence
- Slice
- TranscriptEffect
- Variant
- VariantAnnotation
- VariantCallingAnnotations
- VariantContext

c

org.bdgenomics.adam.sql

# VariantAnnotation 

###
Companion object VariantAnnotation

#### case class VariantAnnotation(ancestralAllele: Option[String] = None, alleleCount: Option[Int] = None, readDepth: Option[Int] = None, forwardReadDepth: Option[Int] = None, reverseReadDepth: Option[Int] = None, referenceReadDepth: Option[Int] = None, referenceForwardReadDepth: Option[Int] = None, referenceReverseReadDepth: Option[Int] = None, alleleFrequency: Option[Float] = None, cigar: Option[String] = None, dbSnp: Option[Boolean] = None, hapMap2: Option[Boolean] = None, hapMap3: Option[Boolean] = None, validated: Option[Boolean] = None, thousandGenomes: Option[Boolean] = None, somatic: Option[Boolean] = None, transcriptEffects: Seq[TranscriptEffect] = Seq(), attributes: Map[String, String] = Map()) extends Product with Serializable

Linear Supertypes
Serializable, Serializable, Product, Equals, AnyRef, Any
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Inherited

1. VariantAnnotation
2. Serializable
3. Serializable
4. Product
5. Equals
6. AnyRef
7. Any

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Visibility

1. Public
2. All

### Instance Constructors

1.  new VariantAnnotation(ancestralAllele: Option[String] = None, alleleCount: Option[Int] = None, readDepth: Option[Int] = None, forwardReadDepth: Option[Int] = None, reverseReadDepth: Option[Int] = None, referenceReadDepth: Option[Int] = None, referenceForwardReadDepth: Option[Int] = None, referenceReverseReadDepth: Option[Int] = None, alleleFrequency: Option[Float] = None, cigar: Option[String] = None, dbSnp: Option[Boolean] = None, hapMap2: Option[Boolean] = None, hapMap3: Option[Boolean] = None, validated: Option[Boolean] = None, thousandGenomes: Option[Boolean] = None, somatic: Option[Boolean] = None, transcriptEffects: Seq[TranscriptEffect] = Seq(), attributes: Map[String, String] = Map())

### 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.  val alleleCount: Option[Int]
5.  val alleleFrequency: Option[Float]
6.  val ancestralAllele: Option[String]
7.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
8.  val attributes: Map[String, String]
9.  def canEqual(that: Any): Boolean
   Definition Classes
     VariantAnnotation → Equals
10.  val cigar: Option[String]
11.  def clone(): AnyRef
    Attributes
      protected[lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native() @HotSpotIntrinsicCandidate()
12.  val dbSnp: Option[Boolean]
13.  final def eq(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
14.  val forwardReadDepth: Option[Int]
15.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
16.  val hapMap2: Option[Boolean]
17.  val hapMap3: Option[Boolean]
18.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
19.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
20.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
21.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
22.  def productArity: Int
    Definition Classes
      VariantAnnotation → Product
23.  def productElement(i: Int): Any
    Definition Classes
      VariantAnnotation → Product
24.  val readDepth: Option[Int]
25.  val referenceForwardReadDepth: Option[Int]
26.  val referenceReadDepth: Option[Int]
27.  val referenceReverseReadDepth: Option[Int]
28.  val reverseReadDepth: Option[Int]
29.  val somatic: Option[Boolean]
30.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
31.  val thousandGenomes: Option[Boolean]
32.  def toAvro: formats.avro.VariantAnnotation
33.  val transcriptEffects: Seq[TranscriptEffect]
34.  val validated: Option[Boolean]
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( ... ) @native()
37.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Deprecated Value Members

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

### Inherited from Serializable

### Inherited from Product

### Inherited from Equals

### Inherited from AnyRef

### Inherited from Any

### Ungrouped