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.

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### Value Members

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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