org.bdgenomics.adam.rdd

# ADAMContext

###
Related Docs: class ADAMContext | package rdd

#### object ADAMContext extends Serializable

This singleton provides an implicit conversion from a SparkContext to the ADAMContext, as well as implicit functions for the Pipe API.

Linear Supertypes
Serializable, Serializable, AnyRef, Any
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. ADAMContext
2. Serializable
3. Serializable
4. AnyRef
5. Any

1. Hide All
2. Show All

Visibility

1. Public
2. All

### 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. #### def ADAMContextFromSession(ss: SparkSession): ADAMContext

   Creates an ADAMContext from a SparkSession.

   Creates an ADAMContext from a SparkSession. Sets active session, including SQLContext, to input session.

   ss

     SparkSession

   returns

     ADAMContext

5. #### implicit def alignmentRecordsToAlignmentRecordsConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset

6. #### implicit def alignmentRecordsToContigsConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset

7. #### implicit def alignmentRecordsToContigsDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset

8. #### implicit def alignmentRecordsToCoverageConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Coverage]): CoverageDataset

9. #### implicit def alignmentRecordsToCoverageDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Coverage]): CoverageDataset

10. #### implicit def alignmentRecordsToFeaturesConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Feature]): FeatureDataset

11. #### implicit def alignmentRecordsToFeaturesDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Feature]): FeatureDataset

12. #### implicit def alignmentRecordsToFragmentsConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Fragment]): FragmentDataset

13. #### implicit def alignmentRecordsToFragmentsDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Fragment]): FragmentDataset

14. #### implicit def alignmentRecordsToGenotypesConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Genotype]): GenotypeDataset

15. #### implicit def alignmentRecordsToGenotypesDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Genotype]): GenotypeDataset

16. #### implicit def alignmentRecordsToVariantContextConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[VariantContext]): VariantContextDataset

17. #### implicit def alignmentRecordsToVariantsConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Variant]): VariantDataset

18. #### implicit def alignmentRecordsToVariantsDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Variant]): VariantDataset

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

    Definition Classes
      Any

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

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

21. #### implicit def contigsToAlignmentRecordsConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset

22. #### implicit def contigsToAlignmentRecordsDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset

23. #### implicit def contigsToContigsConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset

24. #### implicit def contigsToCoverageConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Coverage]): CoverageDataset

25. #### implicit def contigsToCoverageDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Coverage]): CoverageDataset

26. #### implicit def contigsToFeaturesConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Feature]): FeatureDataset

27. #### implicit def contigsToFeaturesDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Feature]): FeatureDataset

28. #### implicit def contigsToFragmentsConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Fragment]): FragmentDataset

29. #### implicit def contigsToFragmentsDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Fragment]): FragmentDataset

30. #### implicit def contigsToGenotypesConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Genotype]): GenotypeDataset

31. #### implicit def contigsToGenotypesDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Genotype]): GenotypeDataset

32. #### implicit def contigsToVariantContextConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[VariantContext]): VariantContextDataset

33. #### implicit def contigsToVariantsConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Variant]): VariantDataset

34. #### implicit def contigsToVariantsDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Variant]): VariantDataset

35. #### implicit def coverageToAlignmentRecordsConversionFn(gDataset: CoverageDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset

36. #### implicit def coverageToAlignmentRecordsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset

37. #### implicit def coverageToContigsConversionFn(gDataset: CoverageDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset

38. #### implicit def coverageToContigsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset

39. #### implicit def coverageToCoverageConversionFn(gDataset: CoverageDataset, rdd: RDD[Coverage]): CoverageDataset

40. #### implicit def coverageToFeaturesConversionFn(gDataset: CoverageDataset, rdd: RDD[Feature]): FeatureDataset

41. #### implicit def coverageToFeaturesDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Feature]): FeatureDataset

42. #### implicit def coverageToFragmentsConversionFn(gDataset: CoverageDataset, rdd: RDD[Fragment]): FragmentDataset

43. #### implicit def coverageToFragmentsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Fragment]): FragmentDataset

44. #### implicit def coverageToGenotypesConversionFn(gDataset: CoverageDataset, rdd: RDD[Genotype]): GenotypeDataset

45. #### implicit def coverageToGenotypesDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Genotype]): GenotypeDataset

46. #### implicit def coverageToVariantContextConversionFn(gDataset: CoverageDataset, rdd: RDD[VariantContext]): VariantContextDataset

47. #### implicit def coverageToVariantsConversionFn(gDataset: CoverageDataset, rdd: RDD[Variant]): VariantDataset

48. #### implicit def coverageToVariantsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Variant]): VariantDataset

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

    Definition Classes
      AnyRef

50. #### def equals(arg0: Any): Boolean

    Definition Classes
      AnyRef → Any

51. #### implicit def featuresToAlignmentRecordsConversionFn(gDataset: FeatureDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset

52. #### implicit def featuresToAlignmentRecordsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset

53. #### implicit def featuresToContigsConversionFn(gDataset: FeatureDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset

54. #### implicit def featuresToContigsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset

55. #### implicit def featuresToCoverageConversionFn(gDataset: FeatureDataset, rdd: RDD[Coverage]): CoverageDataset

56. #### implicit def featuresToCoverageDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Coverage]): CoverageDataset

57. #### implicit def featuresToFeaturesConversionFn(gDataset: FeatureDataset, rdd: RDD[Feature]): FeatureDataset

58. #### implicit def featuresToFragmentsConversionFn(gDataset: FeatureDataset, rdd: RDD[Fragment]): FragmentDataset

59. #### implicit def featuresToFragmentsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Fragment]): FragmentDataset

60. #### implicit def featuresToGenotypesConversionFn(gDataset: FeatureDataset, rdd: RDD[Genotype]): GenotypeDataset

61. #### implicit def featuresToGenotypesDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Genotype]): GenotypeDataset

62. #### implicit def featuresToVariantContextConversionFn(gDataset: FeatureDataset, rdd: RDD[VariantContext]): VariantContextDataset

63. #### implicit def featuresToVariantsConversionFn(gDataset: FeatureDataset, rdd: RDD[Variant]): VariantDataset

64. #### implicit def featuresToVariantsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Variant]): VariantDataset

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

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

66. #### implicit def fragmentsToAlignmentRecordsConversionFn(gDataset: FragmentDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset

67. #### implicit def fragmentsToAlignmentRecordsDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset

68. #### implicit def fragmentsToContigsConversionFn(gDataset: FragmentDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset

69. #### implicit def fragmentsToContigsDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset

70. #### implicit def fragmentsToCoverageConversionFn(gDataset: FragmentDataset, rdd: RDD[Coverage]): CoverageDataset

71. #### implicit def fragmentsToCoverageDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Coverage]): CoverageDataset

72. #### implicit def fragmentsToFeaturesConversionFn(gDataset: FragmentDataset, rdd: RDD[Feature]): FeatureDataset

73. #### implicit def fragmentsToFeaturesDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Feature]): FeatureDataset

74. #### implicit def fragmentsToFragmentsConversionFn(gDataset: FragmentDataset, rdd: RDD[Fragment]): FragmentDataset

75. #### implicit def fragmentsToGenotypesConversionFn(gDataset: FragmentDataset, rdd: RDD[Genotype]): GenotypeDataset

76. #### implicit def fragmentsToGenotypesDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Genotype]): GenotypeDataset

77. #### implicit def fragmentsToVariantContextConversionFn(gDataset: FragmentDataset, rdd: RDD[VariantContext]): VariantContextDataset

78. #### implicit def fragmentsToVariantsConversionFn(gDataset: FragmentDataset, rdd: RDD[Variant]): VariantDataset

79. #### implicit def fragmentsToVariantsDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Variant]): VariantDataset

80. #### implicit def genericToAlignmentRecordsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset

81. #### implicit def genericToContigsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset

82. #### implicit def genericToCoverageConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Coverage]): CoverageDataset

83. #### implicit def genericToFeatureConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Feature]): FeatureDataset

84. #### implicit def genericToFragmentsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Fragment]): FragmentDataset

85. #### implicit def genericToGenotypesConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Genotype]): GenotypeDataset

86. #### implicit def genericToVariantContextsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[VariantContext]): VariantContextDataset

87. #### implicit def genericToVariantsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Variant]): VariantDataset

88. #### implicit def genotypesToAlignmentRecordsConversionFn(gDataset: GenotypeDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset

89. #### implicit def genotypesToAlignmentRecordsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset

90. #### implicit def genotypesToContigsConversionFn(gDataset: GenotypeDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset

91. #### implicit def genotypesToContigsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset

92. #### implicit def genotypesToCoverageConversionFn(gDataset: GenotypeDataset, rdd: RDD[Coverage]): CoverageDataset

93. #### implicit def genotypesToCoverageDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Coverage]): CoverageDataset

94. #### implicit def genotypesToFeaturesConversionFn(gDataset: GenotypeDataset, rdd: RDD[Feature]): FeatureDataset

95. #### implicit def genotypesToFeaturesDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Feature]): FeatureDataset

96. #### implicit def genotypesToFragmentsConversionFn(gDataset: GenotypeDataset, rdd: RDD[Fragment]): FragmentDataset

97. #### implicit def genotypesToFragmentsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Fragment]): FragmentDataset

98. #### implicit def genotypesToGenotypesConversionFn(gDataset: GenotypeDataset, rdd: RDD[Genotype]): GenotypeDataset

99. #### implicit def genotypesToVariantContextConversionFn(gDataset: GenotypeDataset, rdd: RDD[VariantContext]): VariantContextDataset

100. #### implicit def genotypesToVariantsConversionFn(gDataset: GenotypeDataset, rdd: RDD[Variant]): VariantDataset

101. #### implicit def genotypesToVariantsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Variant]): VariantDataset

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

     Definition Classes
       AnyRef → Any

103. #### def hashCode(): Int

     Definition Classes
       AnyRef → Any

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

     Definition Classes
       Any

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

     Definition Classes
       AnyRef

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

     Definition Classes
       AnyRef

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

     Definition Classes
       AnyRef

108. #### implicit def recordToRichRecord(record: AlignmentRecord): RichAlignmentRecord

109. #### implicit def sparkContextToADAMContext(sc: SparkContext): ADAMContext

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

     Definition Classes
       AnyRef

111. #### def toString(): String

     Definition Classes
       AnyRef → Any

112. #### implicit def variantContextsToAlignmentRecordsConversionFn(gDataset: VariantContextDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset

113. #### implicit def variantContextsToContigsConversionFn(gDataset: VariantContextDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset

114. #### implicit def variantContextsToCoverageConversionFn(gDataset: VariantContextDataset, rdd: RDD[Coverage]): CoverageDataset

115. #### implicit def variantContextsToFeaturesConversionFn(gDataset: VariantContextDataset, rdd: RDD[Feature]): FeatureDataset

116. #### implicit def variantContextsToFragmentsConversionFn(gDataset: VariantContextDataset, rdd: RDD[Fragment]): FragmentDataset

117. #### implicit def variantContextsToGenotypesConversionFn(gDataset: VariantContextDataset, rdd: RDD[Genotype]): GenotypeDataset

118. #### implicit def variantContextsToVariantContextsConversionFn(gDataset: VariantContextDataset, rdd: RDD[VariantContext]): VariantContextDataset

119. #### implicit def variantContextsToVariantsConversionFn(gDataset: VariantContextDataset, rdd: RDD[Variant]): VariantDataset

120. #### implicit def variantsToAlignmentRecordsConversionFn(gDataset: VariantDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset

121. #### implicit def variantsToAlignmentRecordsDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset

122. #### implicit def variantsToContigsConversionFn(gDataset: VariantDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset

123. #### implicit def variantsToContigsDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset

124. #### implicit def variantsToCoverageConversionFn(gDataset: VariantDataset, rdd: RDD[Coverage]): CoverageDataset

125. #### implicit def variantsToCoverageDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Coverage]): CoverageDataset

126. #### implicit def variantsToFeaturesConversionFn(gDataset: VariantDataset, rdd: RDD[Feature]): FeatureDataset

127. #### implicit def variantsToFeaturesDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Feature]): FeatureDataset

128. #### implicit def variantsToFragmentsConversionFn(gDataset: VariantDataset, rdd: RDD[Fragment]): FragmentDataset

129. #### implicit def variantsToFragmentsDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Fragment]): FragmentDataset

130. #### implicit def variantsToGenotypesConversionFn(gDataset: VariantDataset, rdd: RDD[Genotype]): GenotypeDataset

131. #### implicit def variantsToGenotypesDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Genotype]): GenotypeDataset

132. #### implicit def variantsToVariantContextConversionFn(gDataset: VariantDataset, rdd: RDD[VariantContext]): VariantContextDataset

133. #### implicit def variantsToVariantsConversionFn(gDataset: VariantDataset, rdd: RDD[Variant]): VariantDataset

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

     Definition Classes
       AnyRef
     Annotations
       @throws( ... )

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

     Definition Classes
       AnyRef
     Annotations
       @throws( ... )

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

     Definition Classes
       AnyRef
     Annotations
       @throws( ... )

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped