org.bdgenomics.adam.rdd

ADAMContext

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: AnyRef): Boolean

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

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  3. final def ##(): Int

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

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

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  6. implicit def alignmentRecordsToContigsConversionFn(gRdd: AlignmentRecordRDD, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentRDD

  7. implicit def alignmentRecordsToContigsDatasetConversionFn(gRdd: AlignmentRecordRDD, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentRDD

  8. implicit def alignmentRecordsToCoverageConversionFn(gRdd: AlignmentRecordRDD, rdd: RDD[Coverage]): CoverageRDD

  9. implicit def alignmentRecordsToCoverageDatasetConversionFn(gRdd: AlignmentRecordRDD, ds: Dataset[Coverage]): CoverageRDD

  10. implicit def alignmentRecordsToFeaturesConversionFn(gRdd: AlignmentRecordRDD, rdd: RDD[Feature]): FeatureRDD

  11. implicit def alignmentRecordsToFeaturesDatasetConversionFn(gRdd: AlignmentRecordRDD, ds: Dataset[Feature]): FeatureRDD

  12. implicit def alignmentRecordsToFragmentsConversionFn(gRdd: AlignmentRecordRDD, rdd: RDD[Fragment]): FragmentRDD

  13. implicit def alignmentRecordsToFragmentsDatasetConversionFn(gRdd: AlignmentRecordRDD, ds: Dataset[Fragment]): FragmentRDD

  14. implicit def alignmentRecordsToGenotypesConversionFn(gRdd: AlignmentRecordRDD, rdd: RDD[Genotype]): GenotypeRDD

  15. implicit def alignmentRecordsToGenotypesDatasetConversionFn(gRdd: AlignmentRecordRDD, ds: Dataset[Genotype]): GenotypeRDD

  16. implicit def alignmentRecordsToVariantContextConversionFn(gRdd: AlignmentRecordRDD, rdd: RDD[VariantContext]): VariantContextRDD

  17. implicit def alignmentRecordsToVariantsConversionFn(gRdd: AlignmentRecordRDD, rdd: RDD[Variant]): VariantRDD

  18. implicit def alignmentRecordsToVariantsDatasetConversionFn(gRdd: AlignmentRecordRDD, ds: Dataset[Variant]): VariantRDD

  19. final def asInstanceOf[T0]: T0

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  20. def clone(): AnyRef

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  21. implicit def contigsToAlignmentRecordsConversionFn(gRdd: NucleotideContigFragmentRDD, rdd: RDD[AlignmentRecord]): AlignmentRecordRDD

  22. implicit def contigsToAlignmentRecordsDatasetConversionFn(gRdd: NucleotideContigFragmentRDD, ds: Dataset[AlignmentRecord]): AlignmentRecordRDD

  23. implicit def contigsToCoverageConversionFn(gRdd: NucleotideContigFragmentRDD, rdd: RDD[Coverage]): CoverageRDD

  24. implicit def contigsToCoverageDatasetConversionFn(gRdd: NucleotideContigFragmentRDD, ds: Dataset[Coverage]): CoverageRDD

  25. implicit def contigsToFeaturesConversionFn(gRdd: NucleotideContigFragmentRDD, rdd: RDD[Feature]): FeatureRDD

  26. implicit def contigsToFeaturesDatasetConversionFn(gRdd: NucleotideContigFragmentRDD, ds: Dataset[Feature]): FeatureRDD

  27. implicit def contigsToFragmentsConversionFn(gRdd: NucleotideContigFragmentRDD, rdd: RDD[Fragment]): FragmentRDD

  28. implicit def contigsToFragmentsDatasetConversionFn(gRdd: NucleotideContigFragmentRDD, ds: Dataset[Fragment]): FragmentRDD

  29. implicit def contigsToGenotypesConversionFn(gRdd: NucleotideContigFragmentRDD, rdd: RDD[Genotype]): GenotypeRDD

  30. implicit def contigsToGenotypesDatasetConversionFn(gRdd: NucleotideContigFragmentRDD, ds: Dataset[Genotype]): GenotypeRDD

  31. implicit def contigsToVariantContextConversionFn(gRdd: NucleotideContigFragmentRDD, rdd: RDD[VariantContext]): VariantContextRDD

  32. implicit def contigsToVariantsConversionFn(gRdd: NucleotideContigFragmentRDD, rdd: RDD[Variant]): VariantRDD

  33. implicit def contigsToVariantsDatasetConversionFn(gRdd: NucleotideContigFragmentRDD, ds: Dataset[Variant]): VariantRDD

  34. implicit def coverageToAlignmentRecordsConversionFn(gRdd: CoverageRDD, rdd: RDD[AlignmentRecord]): AlignmentRecordRDD

  35. implicit def coverageToAlignmentRecordsDatasetConversionFn(gRdd: CoverageRDD, ds: Dataset[AlignmentRecord]): AlignmentRecordRDD

  36. implicit def coverageToContigsConversionFn(gRdd: CoverageRDD, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentRDD

  37. implicit def coverageToContigsDatasetConversionFn(gRdd: CoverageRDD, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentRDD

  38. implicit def coverageToFeaturesConversionFn(gRdd: CoverageRDD, rdd: RDD[Feature]): FeatureRDD

  39. implicit def coverageToFeaturesDatasetConversionFn(gRdd: CoverageRDD, ds: Dataset[Feature]): FeatureRDD

  40. implicit def coverageToFragmentsConversionFn(gRdd: CoverageRDD, rdd: RDD[Fragment]): FragmentRDD

  41. implicit def coverageToFragmentsDatasetConversionFn(gRdd: CoverageRDD, ds: Dataset[Fragment]): FragmentRDD

  42. implicit def coverageToGenotypesConversionFn(gRdd: CoverageRDD, rdd: RDD[Genotype]): GenotypeRDD

  43. implicit def coverageToGenotypesDatasetConversionFn(gRdd: CoverageRDD, ds: Dataset[Genotype]): GenotypeRDD

  44. implicit def coverageToVariantContextConversionFn(gRdd: CoverageRDD, rdd: RDD[VariantContext]): VariantContextRDD

  45. implicit def coverageToVariantsConversionFn(gRdd: CoverageRDD, rdd: RDD[Variant]): VariantRDD

  46. implicit def coverageToVariantsDatasetConversionFn(gRdd: CoverageRDD, ds: Dataset[Variant]): VariantRDD

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

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  48. def equals(arg0: Any): Boolean

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  49. implicit def featuresToAlignmentRecordsConversionFn(gRdd: FeatureRDD, rdd: RDD[AlignmentRecord]): AlignmentRecordRDD

  50. implicit def featuresToAlignmentRecordsDatasetConversionFn(gRdd: FeatureRDD, ds: Dataset[AlignmentRecord]): AlignmentRecordRDD

  51. implicit def featuresToContigsConversionFn(gRdd: FeatureRDD, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentRDD

  52. implicit def featuresToContigsDatasetConversionFn(gRdd: FeatureRDD, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentRDD

  53. implicit def featuresToCoverageConversionFn(gRdd: FeatureRDD, rdd: RDD[Coverage]): CoverageRDD

  54. implicit def featuresToCoverageDatasetConversionFn(gRdd: FeatureRDD, ds: Dataset[Coverage]): CoverageRDD

  55. implicit def featuresToFragmentsConversionFn(gRdd: FeatureRDD, rdd: RDD[Fragment]): FragmentRDD

  56. implicit def featuresToFragmentsDatasetConversionFn(gRdd: FeatureRDD, ds: Dataset[Fragment]): FragmentRDD

  57. implicit def featuresToGenotypesConversionFn(gRdd: FeatureRDD, rdd: RDD[Genotype]): GenotypeRDD

  58. implicit def featuresToGenotypesDatasetConversionFn(gRdd: FeatureRDD, ds: Dataset[Genotype]): GenotypeRDD

  59. implicit def featuresToVariantContextConversionFn(gRdd: FeatureRDD, rdd: RDD[VariantContext]): VariantContextRDD

  60. implicit def featuresToVariantsConversionFn(gRdd: FeatureRDD, rdd: RDD[Variant]): VariantRDD

  61. implicit def featuresToVariantsDatasetConversionFn(gRdd: FeatureRDD, ds: Dataset[Variant]): VariantRDD

  62. def finalize(): Unit

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  63. implicit def fragmentsToAlignmentRecordsConversionFn(gRdd: FragmentRDD, rdd: RDD[AlignmentRecord]): AlignmentRecordRDD

  64. implicit def fragmentsToAlignmentRecordsDatasetConversionFn(gRdd: FragmentRDD, ds: Dataset[AlignmentRecord]): AlignmentRecordRDD

  65. implicit def fragmentsToContigsConversionFn(gRdd: FragmentRDD, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentRDD

  66. implicit def fragmentsToContigsDatasetConversionFn(gRdd: FragmentRDD, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentRDD

  67. implicit def fragmentsToCoverageConversionFn(gRdd: FragmentRDD, rdd: RDD[Coverage]): CoverageRDD

  68. implicit def fragmentsToCoverageDatasetConversionFn(gRdd: FragmentRDD, ds: Dataset[Coverage]): CoverageRDD

  69. implicit def fragmentsToFeaturesConversionFn(gRdd: FragmentRDD, rdd: RDD[Feature]): FeatureRDD

  70. implicit def fragmentsToFeaturesDatasetConversionFn(gRdd: FragmentRDD, ds: Dataset[Feature]): FeatureRDD

  71. implicit def fragmentsToGenotypesConversionFn(gRdd: FragmentRDD, rdd: RDD[Genotype]): GenotypeRDD

  72. implicit def fragmentsToGenotypesDatasetConversionFn(gRdd: FragmentRDD, ds: Dataset[Genotype]): GenotypeRDD

  73. implicit def fragmentsToVariantContextConversionFn(gRdd: FragmentRDD, rdd: RDD[VariantContext]): VariantContextRDD

  74. implicit def fragmentsToVariantsConversionFn(gRdd: FragmentRDD, rdd: RDD[Variant]): VariantRDD

  75. implicit def fragmentsToVariantsDatasetConversionFn(gRdd: FragmentRDD, ds: Dataset[Variant]): VariantRDD

  76. implicit def genericToAlignmentRecordsConversionFn[Y <: GenericGenomicRDD[_]](gRdd: Y, rdd: RDD[AlignmentRecord]): AlignmentRecordRDD

  77. implicit def genericToContigsConversionFn[Y <: GenericGenomicRDD[_]](gRdd: Y, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentRDD

  78. implicit def genericToCoverageConversionFn[Y <: GenericGenomicRDD[_]](gRdd: Y, rdd: RDD[Coverage]): CoverageRDD

  79. implicit def genericToFeatureConversionFn[Y <: GenericGenomicRDD[_]](gRdd: Y, rdd: RDD[Feature]): FeatureRDD

  80. implicit def genericToFragmentsConversionFn[Y <: GenericGenomicRDD[_]](gRdd: Y, rdd: RDD[Fragment]): FragmentRDD

  81. implicit def genericToGenotypesConversionFn[Y <: GenericGenomicRDD[_]](gRdd: Y, rdd: RDD[Genotype]): GenotypeRDD

  82. implicit def genericToVariantContextsConversionFn[Y <: GenericGenomicRDD[_]](gRdd: Y, rdd: RDD[VariantContext]): VariantContextRDD

  83. implicit def genericToVariantsConversionFn[Y <: GenericGenomicRDD[_]](gRdd: Y, rdd: RDD[Variant]): VariantRDD

  84. implicit def genotypesToAlignmentRecordsConversionFn(gRdd: GenotypeRDD, rdd: RDD[AlignmentRecord]): AlignmentRecordRDD

  85. implicit def genotypesToAlignmentRecordsDatasetConversionFn(gRdd: GenotypeRDD, ds: Dataset[AlignmentRecord]): AlignmentRecordRDD

  86. implicit def genotypesToContigsConversionFn(gRdd: GenotypeRDD, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentRDD

  87. implicit def genotypesToContigsDatasetConversionFn(gRdd: GenotypeRDD, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentRDD

  88. implicit def genotypesToCoverageConversionFn(gRdd: GenotypeRDD, rdd: RDD[Coverage]): CoverageRDD

  89. implicit def genotypesToCoverageDatasetConversionFn(gRdd: GenotypeRDD, ds: Dataset[Coverage]): CoverageRDD

  90. implicit def genotypesToFeaturesConversionFn(gRdd: GenotypeRDD, rdd: RDD[Feature]): FeatureRDD

  91. implicit def genotypesToFeaturesDatasetConversionFn(gRdd: GenotypeRDD, ds: Dataset[Feature]): FeatureRDD

  92. implicit def genotypesToFragmentsConversionFn(gRdd: GenotypeRDD, rdd: RDD[Fragment]): FragmentRDD

  93. implicit def genotypesToFragmentsDatasetConversionFn(gRdd: GenotypeRDD, ds: Dataset[Fragment]): FragmentRDD

  94. implicit def genotypesToVariantContextConversionFn(gRdd: GenotypeRDD, rdd: RDD[VariantContext]): VariantContextRDD

  95. implicit def genotypesToVariantsConversionFn(gRdd: GenotypeRDD, rdd: RDD[Variant]): VariantRDD

  96. implicit def genotypesToVariantsDatasetConversionFn(gRdd: GenotypeRDD, ds: Dataset[Variant]): VariantRDD

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

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  98. def hashCode(): Int

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  99. final def isInstanceOf[T0]: Boolean

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

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  101. final def notify(): Unit

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  102. final def notifyAll(): Unit

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  103. implicit def rddToADAMRDD[T](rdd: RDD[T])(implicit ev1: (T) ⇒ IndexedRecord, ev2: Manifest[T]): ConcreteADAMRDDFunctions[T]

  104. implicit def recordToRichRecord(record: AlignmentRecord): RichAlignmentRecord

  105. implicit def sameTypeConversionFn[T, U <: GenomicRDD[T, U]](gRdd: U, rdd: RDD[T]): U

  106. implicit def sparkContextToADAMContext(sc: SparkContext): ADAMContext

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

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  108. def toString(): String

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  109. implicit def variantContextsToAlignmentRecordsConversionFn(gRdd: VariantContextRDD, rdd: RDD[AlignmentRecord]): AlignmentRecordRDD

  110. implicit def variantContextsToContigsConversionFn(gRdd: VariantContextRDD, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentRDD

  111. implicit def variantContextsToCoverageConversionFn(gRdd: VariantContextRDD, rdd: RDD[Coverage]): CoverageRDD

  112. implicit def variantContextsToFeaturesConversionFn(gRdd: VariantContextRDD, rdd: RDD[Feature]): FeatureRDD

  113. implicit def variantContextsToFragmentsConversionFn(gRdd: VariantContextRDD, rdd: RDD[Fragment]): FragmentRDD

  114. implicit def variantContextsToGenotypesConversionFn(gRdd: VariantContextRDD, rdd: RDD[Genotype]): GenotypeRDD

  115. implicit def variantContextsToVariantsConversionFn(gRdd: VariantContextRDD, rdd: RDD[Variant]): VariantRDD

  116. implicit def variantsToAlignmentRecordsConversionFn(gRdd: VariantRDD, rdd: RDD[AlignmentRecord]): AlignmentRecordRDD

  117. implicit def variantsToAlignmentRecordsDatasetConversionFn(gRdd: VariantRDD, ds: Dataset[AlignmentRecord]): AlignmentRecordRDD

  118. implicit def variantsToContigsConversionFn(gRdd: VariantRDD, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentRDD

  119. implicit def variantsToContigsDatasetConversionFn(gRdd: VariantRDD, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentRDD

  120. implicit def variantsToCoverageConversionFn(gRdd: VariantRDD, rdd: RDD[Coverage]): CoverageRDD

  121. implicit def variantsToCoverageDatasetConversionFn(gRdd: VariantRDD, ds: Dataset[Coverage]): CoverageRDD

  122. implicit def variantsToFeaturesConversionFn(gRdd: VariantRDD, rdd: RDD[Feature]): FeatureRDD

  123. implicit def variantsToFeaturesDatasetConversionFn(gRdd: VariantRDD, ds: Dataset[Feature]): FeatureRDD

  124. implicit def variantsToFragmentsConversionFn(gRdd: VariantRDD, rdd: RDD[Fragment]): FragmentRDD

  125. implicit def variantsToFragmentsDatasetConversionFn(gRdd: VariantRDD, ds: Dataset[Fragment]): FragmentRDD

  126. implicit def variantsToGenotypesConversionFn(gRdd: VariantRDD, rdd: RDD[Genotype]): GenotypeRDD

  127. implicit def variantsToGenotypesDatasetConversionFn(gRdd: VariantRDD, ds: Dataset[Genotype]): GenotypeRDD

  128. implicit def variantsToVariantContextConversionFn(gRdd: VariantRDD, rdd: RDD[VariantContext]): VariantContextRDD

  129. final def wait(): Unit

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

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

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