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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