org.bdgenomics.adam.api

# java

#### package java

Visibility

1. Public
2. All

### Type Members

1. #### final class AlignmentRecordsToAlignmentRecordsConverter extends Function2[AlignmentRecordRDD, RDD[AlignmentRecord], AlignmentRecordRDD]

2. #### final class AlignmentRecordsToContigsConverter extends Function2[AlignmentRecordRDD, RDD[NucleotideContigFragment], NucleotideContigFragmentRDD]

3. #### final class AlignmentRecordsToContigsDatasetConverter extends ToContigDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD]

4. #### final class AlignmentRecordsToCoverageConverter extends Function2[AlignmentRecordRDD, RDD[Coverage], CoverageRDD]

5. #### final class AlignmentRecordsToCoverageDatasetConverter extends ToCoverageDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD]

6. #### final class AlignmentRecordsToFeaturesConverter extends Function2[AlignmentRecordRDD, RDD[Feature], FeatureRDD]

7. #### final class AlignmentRecordsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD]

8. #### final class AlignmentRecordsToFragmentsConverter extends Function2[AlignmentRecordRDD, RDD[Fragment], FragmentRDD]

9. #### final class AlignmentRecordsToFragmentsDatasetConverter extends ToFragmentDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD]

10. #### final class AlignmentRecordsToGenotypesConverter extends Function2[AlignmentRecordRDD, RDD[Genotype], GenotypeRDD]

11. #### final class AlignmentRecordsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD]

12. #### final class AlignmentRecordsToVariantContextConverter extends Function2[AlignmentRecordRDD, RDD[VariantContext], VariantContextRDD]

13. #### final class AlignmentRecordsToVariantsConverter extends Function2[AlignmentRecordRDD, RDD[Variant], VariantRDD]

14. #### final class AlignmentRecordsToVariantsDatasetConverter extends ToVariantDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD]

15. #### final class ContigsToAlignmentRecordsConverter extends Function2[NucleotideContigFragmentRDD, RDD[AlignmentRecord], AlignmentRecordRDD]

16. #### final class ContigsToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD]

17. #### final class ContigsToContigsConverter extends Function2[NucleotideContigFragmentRDD, RDD[NucleotideContigFragment], NucleotideContigFragmentRDD]

18. #### final class ContigsToCoverageConverter extends Function2[NucleotideContigFragmentRDD, RDD[Coverage], CoverageRDD]

19. #### final class ContigsToCoverageDatasetConverter extends ToCoverageDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD]

20. #### final class ContigsToFeaturesConverter extends Function2[NucleotideContigFragmentRDD, RDD[Feature], FeatureRDD]

21. #### final class ContigsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD]

22. #### final class ContigsToFragmentsConverter extends Function2[NucleotideContigFragmentRDD, RDD[Fragment], FragmentRDD]

23. #### final class ContigsToFragmentsDatasetConverter extends ToFragmentDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD]

24. #### final class ContigsToGenotypesConverter extends Function2[NucleotideContigFragmentRDD, RDD[Genotype], GenotypeRDD]

25. #### final class ContigsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD]

26. #### final class ContigsToVariantContextsConverter extends Function2[NucleotideContigFragmentRDD, RDD[VariantContext], VariantContextRDD]

27. #### final class ContigsToVariantsConverter extends Function2[NucleotideContigFragmentRDD, RDD[Variant], VariantRDD]

28. #### final class ContigsToVariantsDatasetConverter extends ToVariantDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD]

29. #### final class CoverageToAlignmentRecordsConverter extends Function2[CoverageRDD, RDD[AlignmentRecord], AlignmentRecordRDD]

30. #### final class CoverageToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Coverage, Coverage, CoverageRDD]

31. #### final class CoverageToContigsConverter extends Function2[CoverageRDD, RDD[NucleotideContigFragment], NucleotideContigFragmentRDD]

32. #### final class CoverageToContigsDatasetConverter extends ToContigDatasetConversion[Coverage, Coverage, CoverageRDD]

33. #### final class CoverageToCoverageConverter extends Function2[CoverageRDD, RDD[Coverage], CoverageRDD]

34. #### final class CoverageToFeaturesConverter extends Function2[CoverageRDD, RDD[Feature], FeatureRDD]

35. #### final class CoverageToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Coverage, Coverage, CoverageRDD]

36. #### final class CoverageToFragmentsConverter extends Function2[CoverageRDD, RDD[Fragment], FragmentRDD]

37. #### final class CoverageToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Coverage, Coverage, CoverageRDD]

38. #### final class CoverageToGenotypesConverter extends Function2[CoverageRDD, RDD[Genotype], GenotypeRDD]

39. #### final class CoverageToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Coverage, Coverage, CoverageRDD]

40. #### final class CoverageToVariantContextConverter extends Function2[CoverageRDD, RDD[VariantContext], VariantContextRDD]

41. #### final class CoverageToVariantsConverter extends Function2[CoverageRDD, RDD[Variant], VariantRDD]

42. #### final class CoverageToVariantsDatasetConverter extends ToVariantDatasetConversion[Coverage, Coverage, CoverageRDD]

43. #### final class FeaturesToAlignmentRecordsConverter extends Function2[FeatureRDD, RDD[AlignmentRecord], AlignmentRecordRDD]

44. #### final class FeaturesToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Feature, Feature, FeatureRDD]

45. #### final class FeaturesToContigsConverter extends Function2[FeatureRDD, RDD[NucleotideContigFragment], NucleotideContigFragmentRDD]

46. #### final class FeaturesToContigsDatasetConverter extends ToContigDatasetConversion[Feature, Feature, FeatureRDD]

47. #### final class FeaturesToCoverageConverter extends Function2[FeatureRDD, RDD[Coverage], CoverageRDD]

48. #### final class FeaturesToCoverageDatasetConverter extends ToCoverageDatasetConversion[Feature, Feature, FeatureRDD]

49. #### final class FeaturesToFeatureConverter extends Function2[FeatureRDD, RDD[Feature], FeatureRDD]

50. #### final class FeaturesToFragmentsConverter extends Function2[FeatureRDD, RDD[Fragment], FragmentRDD]

51. #### final class FeaturesToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Feature, Feature, FeatureRDD]

52. #### final class FeaturesToGenotypesConverter extends Function2[FeatureRDD, RDD[Genotype], GenotypeRDD]

53. #### final class FeaturesToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Feature, Feature, FeatureRDD]

54. #### final class FeaturesToVariantContextConverter extends Function2[FeatureRDD, RDD[VariantContext], VariantContextRDD]

55. #### final class FeaturesToVariantsConverter extends Function2[FeatureRDD, RDD[Variant], VariantRDD]

56. #### final class FeaturesToVariantsDatasetConverter extends ToVariantDatasetConversion[Feature, Feature, FeatureRDD]

57. #### final class FragmentsToAlignmentRecordsConverter extends Function2[FragmentRDD, RDD[AlignmentRecord], AlignmentRecordRDD]

58. #### final class FragmentsToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Fragment, Fragment, FragmentRDD]

59. #### final class FragmentsToContigsConverter extends Function2[FragmentRDD, RDD[NucleotideContigFragment], NucleotideContigFragmentRDD]

60. #### final class FragmentsToContigsDatasetConverter extends ToContigDatasetConversion[Fragment, Fragment, FragmentRDD]

61. #### final class FragmentsToCoverageConverter extends Function2[FragmentRDD, RDD[Coverage], CoverageRDD]

62. #### final class FragmentsToCoverageDatasetConverter extends ToCoverageDatasetConversion[Fragment, Fragment, FragmentRDD]

63. #### final class FragmentsToFeaturesConverter extends Function2[FragmentRDD, RDD[Feature], FeatureRDD]

64. #### final class FragmentsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Fragment, Fragment, FragmentRDD]

65. #### final class FragmentsToFragmentsConverter extends Function2[FragmentRDD, RDD[Fragment], FragmentRDD]

66. #### final class FragmentsToGenotypesConverter extends Function2[FragmentRDD, RDD[Genotype], GenotypeRDD]

67. #### final class FragmentsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Fragment, Fragment, FragmentRDD]

68. #### final class FragmentsToVariantContextConverter extends Function2[FragmentRDD, RDD[VariantContext], VariantContextRDD]

69. #### final class FragmentsToVariantsConverter extends Function2[FragmentRDD, RDD[Variant], VariantRDD]

70. #### final class FragmentsToVariantsDatasetConverter extends ToVariantDatasetConversion[Fragment, Fragment, FragmentRDD]

71. #### final class GenotypesToAlignmentRecordsConverter extends Function2[GenotypeRDD, RDD[AlignmentRecord], AlignmentRecordRDD]

72. #### final class GenotypesToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Genotype, Genotype, GenotypeRDD]

73. #### final class GenotypesToContigsConverter extends Function2[GenotypeRDD, RDD[NucleotideContigFragment], NucleotideContigFragmentRDD]

74. #### final class GenotypesToContigsDatasetConverter extends ToContigDatasetConversion[Genotype, Genotype, GenotypeRDD]

75. #### final class GenotypesToCoverageConverter extends Function2[GenotypeRDD, RDD[Coverage], CoverageRDD]

76. #### final class GenotypesToCoverageDatasetConverter extends ToCoverageDatasetConversion[Genotype, Genotype, GenotypeRDD]

77. #### final class GenotypesToFeaturesConverter extends Function2[GenotypeRDD, RDD[Feature], FeatureRDD]

78. #### final class GenotypesToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Genotype, Genotype, GenotypeRDD]

79. #### final class GenotypesToFragmentsConverter extends Function2[GenotypeRDD, RDD[Fragment], FragmentRDD]

80. #### final class GenotypesToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Genotype, Genotype, GenotypeRDD]

81. #### final class GenotypesToGenotypesConverter extends Function2[GenotypeRDD, RDD[Genotype], GenotypeRDD]

82. #### final class GenotypesToVariantContextConverter extends Function2[GenotypeRDD, RDD[VariantContext], VariantContextRDD]

83. #### final class GenotypesToVariantsConverter extends Function2[GenotypeRDD, RDD[Variant], VariantRDD]

84. #### final class GenotypesToVariantsDatasetConverter extends ToVariantDatasetConversion[Genotype, Genotype, GenotypeRDD]

85. #### class JavaADAMContext extends Serializable

    The JavaADAMContext provides java-friendly functions on top of ADAMContext.

86. #### trait ToAlignmentRecordDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, AlignmentRecord, AlignmentRecord, AlignmentRecordRDD]

87. #### trait ToContigDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD]

88. #### trait ToCoverageDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Coverage, Coverage, CoverageRDD]

89. #### trait ToFeatureDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Feature, Feature, FeatureRDD]

90. #### trait ToFragmentDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Fragment, Fragment, FragmentRDD]

91. #### trait ToGenotypeDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Genotype, Genotype, GenotypeRDD]

92. #### trait ToVariantContextDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, VariantContext, VariantContext, VariantContextRDD]

93. #### trait ToVariantDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Variant, Variant, VariantRDD]

94. #### final class VariantContextsToAlignmentRecordsConverter extends Function2[VariantContextRDD, RDD[AlignmentRecord], AlignmentRecordRDD]

95. #### final class VariantContextsToContigsConverter extends Function2[VariantContextRDD, RDD[NucleotideContigFragment], NucleotideContigFragmentRDD]

96. #### final class VariantContextsToCoverageConverter extends Function2[VariantContextRDD, RDD[Coverage], CoverageRDD]

97. #### final class VariantContextsToFeaturesConverter extends Function2[VariantContextRDD, RDD[Feature], FeatureRDD]

98. #### final class VariantContextsToFragmentsConverter extends Function2[VariantContextRDD, RDD[Fragment], FragmentRDD]

99. #### final class VariantContextsToGenotypesConverter extends Function2[VariantContextRDD, RDD[Genotype], GenotypeRDD]

100. #### final class VariantContextsToVariantContextConverter extends Function2[VariantContextRDD, RDD[VariantContext], VariantContextRDD]

101. #### final class VariantContextsToVariantsConverter extends Function2[VariantContextRDD, RDD[Variant], VariantRDD]

102. #### final class VariantsToAlignmentRecordsConverter extends Function2[VariantRDD, RDD[AlignmentRecord], AlignmentRecordRDD]

103. #### final class VariantsToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Variant, Variant, VariantRDD]

104. #### final class VariantsToContigsConverter extends Function2[VariantRDD, RDD[NucleotideContigFragment], NucleotideContigFragmentRDD]

105. #### final class VariantsToContigsDatasetConverter extends ToContigDatasetConversion[Variant, Variant, VariantRDD]

106. #### final class VariantsToCoverageConverter extends Function2[VariantRDD, RDD[Coverage], CoverageRDD]

107. #### final class VariantsToCoverageDatasetConverter extends ToCoverageDatasetConversion[Variant, Variant, VariantRDD]

108. #### final class VariantsToFeaturesConverter extends Function2[VariantRDD, RDD[Feature], FeatureRDD]

109. #### final class VariantsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Variant, Variant, VariantRDD]

110. #### final class VariantsToFragmentsConverter extends Function2[VariantRDD, RDD[Fragment], FragmentRDD]

111. #### final class VariantsToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Variant, Variant, VariantRDD]

112. #### final class VariantsToGenotypesConverter extends Function2[VariantRDD, RDD[Genotype], GenotypeRDD]

113. #### final class VariantsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Variant, Variant, VariantRDD]

114. #### final class VariantsToVariantContextConverter extends Function2[VariantRDD, RDD[VariantContext], VariantContextRDD]

115. #### final class VariantsToVariantsConverter extends Function2[VariantRDD, RDD[Variant], VariantRDD]

### Value Members

1. #### object JavaADAMContext extends Serializable

### Ungrouped