org.bdgenomics.adam.sql

# Genotype

###
Related Docs: object Genotype | package sql

#### case class Genotype(variant: Option[Variant] = None, contigName: Option[String] = None, start: Option[Long] = None, end: Option[Long] = None, variantCallingAnnotations: Option[VariantCallingAnnotations] = None, sampleId: Option[String] = None, sampleDescription: Option[String] = None, processingDescription: Option[String] = None, alleles: Seq[String] = Seq(), expectedAlleleDosage: Option[Float] = None, referenceReadDepth: Option[Int] = None, alternateReadDepth: Option[Int] = None, readDepth: Option[Int] = None, minReadDepth: Option[Int] = None, genotypeQuality: Option[Int] = None, genotypeLikelihoods: Seq[Double] = Seq(), nonReferenceLikelihoods: Seq[Double] = Seq(), strandBiasComponents: Seq[Int] = Seq(), splitFromMultiAllelic: Option[Boolean] = None, phased: Option[Boolean] = None, phaseSetId: Option[Int] = None, phaseQuality: Option[Int] = None) extends Product with Serializable

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

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

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Visibility

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2. All

### Instance Constructors

1. #### new Genotype(variant: Option[Variant] = None, contigName: Option[String] = None, start: Option[Long] = None, end: Option[Long] = None, variantCallingAnnotations: Option[VariantCallingAnnotations] = None, sampleId: Option[String] = None, sampleDescription: Option[String] = None, processingDescription: Option[String] = None, alleles: Seq[String] = Seq(), expectedAlleleDosage: Option[Float] = None, referenceReadDepth: Option[Int] = None, alternateReadDepth: Option[Int] = None, readDepth: Option[Int] = None, minReadDepth: Option[Int] = None, genotypeQuality: Option[Int] = None, genotypeLikelihoods: Seq[Double] = Seq(), nonReferenceLikelihoods: Seq[Double] = Seq(), strandBiasComponents: Seq[Int] = Seq(), splitFromMultiAllelic: Option[Boolean] = None, phased: Option[Boolean] = None, phaseSetId: Option[Int] = None, phaseQuality: Option[Int] = 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 alleles: Seq[String]

5. #### val alternateReadDepth: Option[Int]

6. #### final def asInstanceOf[T0]: T0

   Definition Classes
     Any

7. #### def canEqual(that: Any): Boolean

   Definition Classes
     Genotype → Equals

8. #### def clone(): AnyRef

   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... )

9. #### val contigName: Option[String]

10. #### val end: Option[Long]

11. #### final def eq(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

12. #### val expectedAlleleDosage: Option[Float]

13. #### def finalize(): Unit

    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )

14. #### val genotypeLikelihoods: Seq[Double]

15. #### val genotypeQuality: Option[Int]

16. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

17. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

18. #### val minReadDepth: Option[Int]

19. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

20. #### val nonReferenceLikelihoods: Seq[Double]

21. #### final def notify(): Unit

    Definition Classes
      AnyRef

22. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

23. #### val phaseQuality: Option[Int]

24. #### val phaseSetId: Option[Int]

25. #### val phased: Option[Boolean]

26. #### val processingDescription: Option[String]

27. #### def productArity: Int

    Definition Classes
      Genotype → Product

28. #### def productElement(i: Int): Any

    Definition Classes
      Genotype → Product

29. #### val readDepth: Option[Int]

30. #### val referenceReadDepth: Option[Int]

31. #### val sampleDescription: Option[String]

32. #### val sampleId: Option[String]

33. #### val splitFromMultiAllelic: Option[Boolean]

34. #### val start: Option[Long]

35. #### val strandBiasComponents: Seq[Int]

36. #### final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
      AnyRef

37. #### def toAvro: formats.avro.Genotype

38. #### val variant: Option[Variant]

39. #### val variantCallingAnnotations: Option[VariantCallingAnnotations]

40. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

41. #### final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

42. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from Serializable

### Inherited from Product

### Inherited from Equals

### Inherited from AnyRef

### Inherited from Any

### Ungrouped