org.bdgenomics.adam.avro

VariantCallingAnnotations

class VariantCallingAnnotations extends SpecificRecordBase with SpecificRecord

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

  1. new VariantCallingAnnotations(readDepth: Integer, downsampled: Boolean, baseQRankSum: Float, clippingRankSum: Float, fisherStrandBiasPValue: Float, haplotypeScore: Float, inbreedingCoefficient: Float, alleleCountMLE: List[Integer], alleleFrequencyMLE: List[Integer], rmsMapQ: Float, mapq0Reads: Integer, mqRankSum: Float, usedForNegativeTrainingSet: Boolean, usedForPositiveTrainingSet: Boolean, variantQualityByDepth: Float, readPositionRankSum: Float, vqslod: Float, culprit: CharSequence, variantCallErrorProbability: Float, variantIsPassing: Boolean, variantFilters: List[CharSequence])

  2. new VariantCallingAnnotations()

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
    VariantCallingAnnotations → SpecificRecordBase → IndexedRecord

  13. def getAlleleCountMLE(): List[Integer]

  14. def getAlleleFrequencyMLE(): List[Integer]

  15. def getBaseQRankSum(): Float

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

    Definition Classes
    AnyRef → Any

  17. def getClippingRankSum(): Float

  18. def getCulprit(): CharSequence

  19. def getDownsampled(): Boolean

  20. def getFisherStrandBiasPValue(): Float

  21. def getHaplotypeScore(): Float

  22. def getInbreedingCoefficient(): Float

  23. def getMapq0Reads(): Integer

  24. def getMqRankSum(): Float

  25. def getReadDepth(): Integer

  26. def getReadPositionRankSum(): Float

  27. def getRmsMapQ(): Float

  28. def getSchema(): Schema

    Definition Classes
    VariantCallingAnnotations → SpecificRecordBase → GenericContainer

  29. def getUsedForNegativeTrainingSet(): Boolean

  30. def getUsedForPositiveTrainingSet(): Boolean

  31. def getVariantCallErrorProbability(): Float

  32. def getVariantFilters(): List[CharSequence]

  33. def getVariantIsPassing(): Boolean

  34. def getVariantQualityByDepth(): Float

  35. def getVqslod(): Float

  36. def hashCode(): Int

    Definition Classes
    SpecificRecordBase → AnyRef → Any

  37. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  39. final def notify(): Unit

    Definition Classes
    AnyRef

  40. final def notifyAll(): Unit

    Definition Classes
    AnyRef

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

    Definition Classes
    VariantCallingAnnotations → SpecificRecordBase → IndexedRecord

  42. def setAlleleCountMLE(value: List[Integer]): Unit

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

  44. def setBaseQRankSum(value: Float): Unit

  45. def setClippingRankSum(value: Float): Unit

  46. def setCulprit(value: CharSequence): Unit

  47. def setDownsampled(value: Boolean): Unit

  48. def setFisherStrandBiasPValue(value: Float): Unit

  49. def setHaplotypeScore(value: Float): Unit

  50. def setInbreedingCoefficient(value: Float): Unit

  51. def setMapq0Reads(value: Integer): Unit

  52. def setMqRankSum(value: Float): Unit

  53. def setReadDepth(value: Integer): Unit

  54. def setReadPositionRankSum(value: Float): Unit

  55. def setRmsMapQ(value: Float): Unit

  56. def setUsedForNegativeTrainingSet(value: Boolean): Unit

  57. def setUsedForPositiveTrainingSet(value: Boolean): Unit

  58. def setVariantCallErrorProbability(value: Float): Unit

  59. def setVariantFilters(value: List[CharSequence]): Unit

  60. def setVariantIsPassing(value: Boolean): Unit

  61. def setVariantQualityByDepth(value: Float): Unit

  62. def setVqslod(value: Float): Unit

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

    Definition Classes
    AnyRef

  64. def toString(): String

    Definition Classes
    SpecificRecordBase → AnyRef → Any

  65. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  67. 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

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