org.bdgenomics.adam.avro

ADAMGenotype

class ADAMGenotype extends SpecificRecordBase with SpecificRecord

Linear Supertypes
SpecificRecordBase, Comparable[SpecificRecord], SpecificRecord, IndexedRecord, GenericContainer, AnyRef, Any
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Inherited
  1. ADAMGenotype
  2. SpecificRecordBase
  3. Comparable
  4. SpecificRecord
  5. IndexedRecord
  6. GenericContainer
  7. AnyRef
  8. Any
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Instance Constructors

  1. new ADAMGenotype(variant: ADAMVariant, variantCallingAnnotations: VariantCallingAnnotations, sampleId: CharSequence, sampleDescription: CharSequence, processingDescription: CharSequence, alleles: List[ADAMGenotypeAllele], expectedAlleleDosage: Float, referenceReadDepth: Integer, alternateReadDepth: Integer, readDepth: Integer, minReadDepth: Integer, genotypeQuality: Integer, genotypeLikelihoods: List[Integer], nonReferenceLikelihoods: List[Integer], strandBiasComponents: List[Integer], splitFromMultiAllelic: Boolean, isPhased: Boolean, phaseSetId: Integer, phaseQuality: Integer)

  2. new ADAMGenotype()

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  5. final def ==(arg0: Any): Boolean

    Definition Classes
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def clone(): AnyRef

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

  8. def compareTo(arg0: SpecificRecord): Int

    Definition Classes
    SpecificRecordBase → Comparable

  9. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  10. def equals(arg0: Any): Boolean

    Definition Classes
    SpecificRecordBase → AnyRef → Any

  11. def finalize(): Unit

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

  12. def get(arg0: Int): AnyRef

    Definition Classes
    ADAMGenotype → SpecificRecordBase → IndexedRecord

  13. def getAlleles(): List[ADAMGenotypeAllele]

  14. def getAlternateReadDepth(): Integer

  15. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  16. def getExpectedAlleleDosage(): Float

  17. def getGenotypeLikelihoods(): List[Integer]

  18. def getGenotypeQuality(): Integer

  19. def getIsPhased(): Boolean

  20. def getMinReadDepth(): Integer

  21. def getNonReferenceLikelihoods(): List[Integer]

  22. def getPhaseQuality(): Integer

  23. def getPhaseSetId(): Integer

  24. def getProcessingDescription(): CharSequence

  25. def getReadDepth(): Integer

  26. def getReferenceReadDepth(): Integer

  27. def getSampleDescription(): CharSequence

  28. def getSampleId(): CharSequence

  29. def getSchema(): Schema

    Definition Classes
    ADAMGenotype → SpecificRecordBase → GenericContainer

  30. def getSplitFromMultiAllelic(): Boolean

  31. def getStrandBiasComponents(): List[Integer]

  32. def getVariant(): ADAMVariant

  33. def getVariantCallingAnnotations(): VariantCallingAnnotations

  34. def hashCode(): Int

    Definition Classes
    SpecificRecordBase → AnyRef → Any

  35. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  36. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  37. final def notify(): Unit

    Definition Classes
    AnyRef

  38. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  39. def put(arg0: Int, arg1: Any): Unit

    Definition Classes
    ADAMGenotype → SpecificRecordBase → IndexedRecord

  40. def setAlleles(value: List[ADAMGenotypeAllele]): Unit

  41. def setAlternateReadDepth(value: Integer): Unit

  42. def setExpectedAlleleDosage(value: Float): Unit

  43. def setGenotypeLikelihoods(value: List[Integer]): Unit

  44. def setGenotypeQuality(value: Integer): Unit

  45. def setIsPhased(value: Boolean): Unit

  46. def setMinReadDepth(value: Integer): Unit

  47. def setNonReferenceLikelihoods(value: List[Integer]): Unit

  48. def setPhaseQuality(value: Integer): Unit

  49. def setPhaseSetId(value: Integer): Unit

  50. def setProcessingDescription(value: CharSequence): Unit

  51. def setReadDepth(value: Integer): Unit

  52. def setReferenceReadDepth(value: Integer): Unit

  53. def setSampleDescription(value: CharSequence): Unit

  54. def setSampleId(value: CharSequence): Unit

  55. def setSplitFromMultiAllelic(value: Boolean): Unit

  56. def setStrandBiasComponents(value: List[Integer]): Unit

  57. def setVariant(value: ADAMVariant): Unit

  58. def setVariantCallingAnnotations(value: VariantCallingAnnotations): Unit

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

    Definition Classes
    AnyRef

  60. def toString(): String

    Definition Classes
    SpecificRecordBase → AnyRef → Any

  61. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  63. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from SpecificRecordBase

Inherited from Comparable[SpecificRecord]

Inherited from SpecificRecord

Inherited from IndexedRecord

Inherited from GenericContainer

Inherited from AnyRef

Inherited from Any

Ungrouped