ADAM_2.12: Core 0.36.0 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 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

# Variant 

###
Companion object Variant

#### case class Variant(referenceName: Option[String] = None, start: Option[Long] = None, end: Option[Long] = None, names: Seq[String] = Seq(), splitFromMultiAllelic: Option[Boolean] = None, referenceAllele: Option[String] = None, alternateAllele: Option[String] = None, quality: Option[Double] = None, filtersApplied: Option[Boolean] = None, filtersPassed: Option[Boolean] = None, filtersFailed: Seq[String] = Seq(), annotation: Option[VariantAnnotation] = None) extends Product with Serializable

Linear Supertypes
Serializable, Serializable, Product, Equals, AnyRef, Any
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2. By Inheritance

Inherited

1. Variant
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 Variant(referenceName: Option[String] = None, start: Option[Long] = None, end: Option[Long] = None, names: Seq[String] = Seq(), splitFromMultiAllelic: Option[Boolean] = None, referenceAllele: Option[String] = None, alternateAllele: Option[String] = None, quality: Option[Double] = None, filtersApplied: Option[Boolean] = None, filtersPassed: Option[Boolean] = None, filtersFailed: Seq[String] = Seq(), annotation: Option[VariantAnnotation] = None)

### 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 alternateAllele: Option[String]
5.  val annotation: Option[VariantAnnotation]
6.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
7.  def canEqual(that: Any): Boolean
   Definition Classes
     Variant → Equals
8.  def clone(): AnyRef
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native() @HotSpotIntrinsicCandidate()
9.  val end: Option[Long]
10.  final def eq(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
11.  val filtersApplied: Option[Boolean]
12.  val filtersFailed: Seq[String]
13.  val filtersPassed: Option[Boolean]
14.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
15.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
16.  val names: Seq[String]
17.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
18.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
19.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
20.  def productArity: Int
    Definition Classes
      Variant → Product
21.  def productElement(i: Int): Any
    Definition Classes
      Variant → Product
22.  val quality: Option[Double]
23.  val referenceAllele: Option[String]
24.  val referenceName: Option[String]
25.  val splitFromMultiAllelic: Option[Boolean]
26.  val start: Option[Long]
27.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
28.  def toAvro: formats.avro.Variant
29.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
30.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
31.  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
   Deprecated

     (Since version ) see corresponding Javadoc for more information.

### Inherited from Serializable

### Inherited from Product

### Inherited from Equals

### Inherited from AnyRef

### Inherited from Any

### Ungrouped