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.

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  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
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  3. final def ==(arg0: Any): Boolean
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  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
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  20. def clone(): AnyRef
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  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
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  50. def equals(arg0: Any): Boolean
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  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
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  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[_]
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  103. def hashCode(): Int
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  104. final def isInstanceOf[T0]: Boolean
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  105. final def ne(arg0: AnyRef): Boolean
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  106. final def notify(): Unit
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  107. final def notifyAll(): Unit
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  108. implicit def recordToRichRecord(record: AlignmentRecord): RichAlignmentRecord
  109. implicit def sparkContextToADAMContext(sc: SparkContext): ADAMContext
  110. final def synchronized[T0](arg0: ⇒ T0): T0
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  111. def toString(): String
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  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
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  135. final def wait(arg0: Long, arg1: Int): Unit
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  136. final def wait(arg0: Long): Unit
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