org.bdgenomics.adam.api

# java

#### package java

Visibility

1. Public
2. All

### Type Members

1. #### final class AlignmentsToAlignmentsConverter extends Function2[AlignmentDataset, RDD[Alignment], AlignmentDataset]

2. #### final class AlignmentsToCoverageConverter extends Function2[AlignmentDataset, RDD[Coverage], CoverageDataset]

3. #### final class AlignmentsToCoverageDatasetConverter extends ToCoverageDatasetConversion[Alignment, Alignment, AlignmentDataset]

4. #### final class AlignmentsToFeaturesConverter extends Function2[AlignmentDataset, RDD[Feature], FeatureDataset]

5. #### final class AlignmentsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Alignment, Alignment, AlignmentDataset]

6. #### final class AlignmentsToFragmentsConverter extends Function2[AlignmentDataset, RDD[Fragment], FragmentDataset]

7. #### final class AlignmentsToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Alignment, Alignment, AlignmentDataset]

8. #### final class AlignmentsToGenotypesConverter extends Function2[AlignmentDataset, RDD[Genotype], GenotypeDataset]

9. #### final class AlignmentsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Alignment, Alignment, AlignmentDataset]

10. #### final class AlignmentsToReadsConverter extends Function2[AlignmentDataset, RDD[Read], ReadDataset]

11. #### final class AlignmentsToReadsDatasetConverter extends ToReadDatasetConversion[Alignment, Alignment, AlignmentDataset]

12. #### final class AlignmentsToSequencesConverter extends Function2[AlignmentDataset, RDD[Sequence], SequenceDataset]

13. #### final class AlignmentsToSequencesDatasetConverter extends ToSequenceDatasetConversion[Alignment, Alignment, AlignmentDataset]

14. #### final class AlignmentsToSlicesConverter extends Function2[AlignmentDataset, RDD[Slice], SliceDataset]

15. #### final class AlignmentsToSlicesDatasetConverter extends ToSliceDatasetConversion[Alignment, Alignment, AlignmentDataset]

16. #### final class AlignmentsToVariantContextConverter extends Function2[AlignmentDataset, RDD[VariantContext], VariantContextDataset]

17. #### final class AlignmentsToVariantsConverter extends Function2[AlignmentDataset, RDD[Variant], VariantDataset]

18. #### final class AlignmentsToVariantsDatasetConverter extends ToVariantDatasetConversion[Alignment, Alignment, AlignmentDataset]

19. #### final class CoverageToAlignmentsConverter extends Function2[CoverageDataset, RDD[Alignment], AlignmentDataset]

20. #### final class CoverageToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Coverage, Coverage, CoverageDataset]

21. #### final class CoverageToCoverageConverter extends Function2[CoverageDataset, RDD[Coverage], CoverageDataset]

22. #### final class CoverageToFeaturesConverter extends Function2[CoverageDataset, RDD[Feature], FeatureDataset]

23. #### final class CoverageToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Coverage, Coverage, CoverageDataset]

24. #### final class CoverageToFragmentsConverter extends Function2[CoverageDataset, RDD[Fragment], FragmentDataset]

25. #### final class CoverageToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Coverage, Coverage, CoverageDataset]

26. #### final class CoverageToGenotypesConverter extends Function2[CoverageDataset, RDD[Genotype], GenotypeDataset]

27. #### final class CoverageToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Coverage, Coverage, CoverageDataset]

28. #### final class CoverageToReadsConverter extends Function2[CoverageDataset, RDD[Read], ReadDataset]

29. #### final class CoverageToReadsDatasetConverter extends ToReadDatasetConversion[Coverage, Coverage, CoverageDataset]

30. #### final class CoverageToSequencesConverter extends Function2[CoverageDataset, RDD[Sequence], SequenceDataset]

31. #### final class CoverageToSequencesDatasetConverter extends ToSequenceDatasetConversion[Coverage, Coverage, CoverageDataset]

32. #### final class CoverageToSlicesConverter extends Function2[CoverageDataset, RDD[Slice], SliceDataset]

33. #### final class CoverageToSlicesDatasetConverter extends ToSliceDatasetConversion[Coverage, Coverage, CoverageDataset]

34. #### final class CoverageToVariantContextConverter extends Function2[CoverageDataset, RDD[VariantContext], VariantContextDataset]

35. #### final class CoverageToVariantsConverter extends Function2[CoverageDataset, RDD[Variant], VariantDataset]

36. #### final class CoverageToVariantsDatasetConverter extends ToVariantDatasetConversion[Coverage, Coverage, CoverageDataset]

37. #### final class FeaturesToAlignmentsConverter extends Function2[FeatureDataset, RDD[Alignment], AlignmentDataset]

38. #### final class FeaturesToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Feature, Feature, FeatureDataset]

39. #### final class FeaturesToCoverageConverter extends Function2[FeatureDataset, RDD[Coverage], CoverageDataset]

40. #### final class FeaturesToCoverageDatasetConverter extends ToCoverageDatasetConversion[Feature, Feature, FeatureDataset]

41. #### final class FeaturesToFeatureConverter extends Function2[FeatureDataset, RDD[Feature], FeatureDataset]

42. #### final class FeaturesToFragmentsConverter extends Function2[FeatureDataset, RDD[Fragment], FragmentDataset]

43. #### final class FeaturesToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Feature, Feature, FeatureDataset]

44. #### final class FeaturesToGenotypesConverter extends Function2[FeatureDataset, RDD[Genotype], GenotypeDataset]

45. #### final class FeaturesToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Feature, Feature, FeatureDataset]

46. #### final class FeaturesToReadsConverter extends Function2[FeatureDataset, RDD[Read], ReadDataset]

47. #### final class FeaturesToReadsDatasetConverter extends ToReadDatasetConversion[Feature, Feature, FeatureDataset]

48. #### final class FeaturesToSequencesConverter extends Function2[FeatureDataset, RDD[Sequence], SequenceDataset]

49. #### final class FeaturesToSequencesDatasetConverter extends ToSequenceDatasetConversion[Feature, Feature, FeatureDataset]

50. #### final class FeaturesToSlicesConverter extends Function2[FeatureDataset, RDD[Slice], SliceDataset]

51. #### final class FeaturesToSlicesDatasetConverter extends ToSliceDatasetConversion[Feature, Feature, FeatureDataset]

52. #### final class FeaturesToVariantContextConverter extends Function2[FeatureDataset, RDD[VariantContext], VariantContextDataset]

53. #### final class FeaturesToVariantsConverter extends Function2[FeatureDataset, RDD[Variant], VariantDataset]

54. #### final class FeaturesToVariantsDatasetConverter extends ToVariantDatasetConversion[Feature, Feature, FeatureDataset]

55. #### final class FragmentsToAlignmentsConverter extends Function2[FragmentDataset, RDD[Alignment], AlignmentDataset]

56. #### final class FragmentsToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Fragment, Fragment, FragmentDataset]

57. #### final class FragmentsToCoverageConverter extends Function2[FragmentDataset, RDD[Coverage], CoverageDataset]

58. #### final class FragmentsToCoverageDatasetConverter extends ToCoverageDatasetConversion[Fragment, Fragment, FragmentDataset]

59. #### final class FragmentsToFeaturesConverter extends Function2[FragmentDataset, RDD[Feature], FeatureDataset]

60. #### final class FragmentsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Fragment, Fragment, FragmentDataset]

61. #### final class FragmentsToFragmentsConverter extends Function2[FragmentDataset, RDD[Fragment], FragmentDataset]

62. #### final class FragmentsToGenotypesConverter extends Function2[FragmentDataset, RDD[Genotype], GenotypeDataset]

63. #### final class FragmentsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Fragment, Fragment, FragmentDataset]

64. #### final class FragmentsToReadsConverter extends Function2[FragmentDataset, RDD[Read], ReadDataset]

65. #### final class FragmentsToReadsDatasetConverter extends ToReadDatasetConversion[Fragment, Fragment, FragmentDataset]

66. #### final class FragmentsToSequencesConverter extends Function2[FragmentDataset, RDD[Sequence], SequenceDataset]

67. #### final class FragmentsToSequencesDatasetConverter extends ToSequenceDatasetConversion[Fragment, Fragment, FragmentDataset]

68. #### final class FragmentsToSlicesConverter extends Function2[FragmentDataset, RDD[Slice], SliceDataset]

69. #### final class FragmentsToSlicesDatasetConverter extends ToSliceDatasetConversion[Fragment, Fragment, FragmentDataset]

70. #### final class FragmentsToVariantContextConverter extends Function2[FragmentDataset, RDD[VariantContext], VariantContextDataset]

71. #### final class FragmentsToVariantsConverter extends Function2[FragmentDataset, RDD[Variant], VariantDataset]

72. #### final class FragmentsToVariantsDatasetConverter extends ToVariantDatasetConversion[Fragment, Fragment, FragmentDataset]

73. #### final class GenotypesToAlignmentsConverter extends Function2[GenotypeDataset, RDD[Alignment], AlignmentDataset]

74. #### final class GenotypesToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Genotype, Genotype, GenotypeDataset]

75. #### final class GenotypesToCoverageConverter extends Function2[GenotypeDataset, RDD[Coverage], CoverageDataset]

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

77. #### final class GenotypesToFeaturesConverter extends Function2[GenotypeDataset, RDD[Feature], FeatureDataset]

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

79. #### final class GenotypesToFragmentsConverter extends Function2[GenotypeDataset, RDD[Fragment], FragmentDataset]

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

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

82. #### final class GenotypesToReadsConverter extends Function2[GenotypeDataset, RDD[Read], ReadDataset]

83. #### final class GenotypesToReadsDatasetConverter extends ToReadDatasetConversion[Genotype, Genotype, GenotypeDataset]

84. #### final class GenotypesToSequencesConverter extends Function2[GenotypeDataset, RDD[Sequence], SequenceDataset]

85. #### final class GenotypesToSequencesDatasetConverter extends ToSequenceDatasetConversion[Genotype, Genotype, GenotypeDataset]

86. #### final class GenotypesToSlicesConverter extends Function2[GenotypeDataset, RDD[Slice], SliceDataset]

87. #### final class GenotypesToSlicesDatasetConverter extends ToSliceDatasetConversion[Genotype, Genotype, GenotypeDataset]

88. #### final class GenotypesToVariantContextConverter extends Function2[GenotypeDataset, RDD[VariantContext], VariantContextDataset]

89. #### final class GenotypesToVariantsConverter extends Function2[GenotypeDataset, RDD[Variant], VariantDataset]

90. #### final class GenotypesToVariantsDatasetConverter extends ToVariantDatasetConversion[Genotype, Genotype, GenotypeDataset]

91. #### class JavaADAMContext extends Serializable

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

92. #### final class ReadsToAlignmentsConverter extends Function2[ReadDataset, RDD[Alignment], AlignmentDataset]

93. #### final class ReadsToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Read, Read, ReadDataset]

94. #### final class ReadsToCoverageConverter extends Function2[ReadDataset, RDD[Coverage], CoverageDataset]

95. #### final class ReadsToCoverageDatasetConverter extends ToCoverageDatasetConversion[Read, Read, ReadDataset]

96. #### final class ReadsToFeaturesConverter extends Function2[ReadDataset, RDD[Feature], FeatureDataset]

97. #### final class ReadsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Read, Read, ReadDataset]

98. #### final class ReadsToFragmentsConverter extends Function2[ReadDataset, RDD[Fragment], FragmentDataset]

99. #### final class ReadsToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Read, Read, ReadDataset]

100. #### final class ReadsToGenotypesConverter extends Function2[ReadDataset, RDD[Genotype], GenotypeDataset]

101. #### final class ReadsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Read, Read, ReadDataset]

102. #### final class ReadsToReadsConverter extends Function2[ReadDataset, RDD[Read], ReadDataset]

103. #### final class ReadsToSequencesConverter extends Function2[ReadDataset, RDD[Sequence], SequenceDataset]

104. #### final class ReadsToSequencesDatasetConverter extends ToSequenceDatasetConversion[Read, Read, ReadDataset]

105. #### final class ReadsToSlicesConverter extends Function2[ReadDataset, RDD[Slice], SliceDataset]

106. #### final class ReadsToSlicesDatasetConverter extends ToSliceDatasetConversion[Read, Read, ReadDataset]

107. #### final class ReadsToVariantContextsConverter extends Function2[ReadDataset, RDD[VariantContext], VariantContextDataset]

108. #### final class ReadsToVariantsConverter extends Function2[ReadDataset, RDD[Variant], VariantDataset]

109. #### final class ReadsToVariantsDatasetConverter extends ToVariantDatasetConversion[Read, Read, ReadDataset]

110. #### final class SequencesToAlignmentsConverter extends Function2[SequenceDataset, RDD[Alignment], AlignmentDataset]

111. #### final class SequencesToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Sequence, Sequence, SequenceDataset]

112. #### final class SequencesToCoverageConverter extends Function2[SequenceDataset, RDD[Coverage], CoverageDataset]

113. #### final class SequencesToCoverageDatasetConverter extends ToCoverageDatasetConversion[Sequence, Sequence, SequenceDataset]

114. #### final class SequencesToFeaturesConverter extends Function2[SequenceDataset, RDD[Feature], FeatureDataset]

115. #### final class SequencesToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Sequence, Sequence, SequenceDataset]

116. #### final class SequencesToFragmentsConverter extends Function2[SequenceDataset, RDD[Fragment], FragmentDataset]

117. #### final class SequencesToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Sequence, Sequence, SequenceDataset]

118. #### final class SequencesToGenotypesConverter extends Function2[SequenceDataset, RDD[Genotype], GenotypeDataset]

119. #### final class SequencesToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Sequence, Sequence, SequenceDataset]

120. #### final class SequencesToReadsConverter extends Function2[SequenceDataset, RDD[Read], ReadDataset]

121. #### final class SequencesToReadsDatasetConverter extends ToReadDatasetConversion[Sequence, Sequence, SequenceDataset]

122. #### final class SequencesToSequencesConverter extends Function2[SequenceDataset, RDD[Sequence], SequenceDataset]

123. #### final class SequencesToSlicesConverter extends Function2[SequenceDataset, RDD[Slice], SliceDataset]

124. #### final class SequencesToSlicesDatasetConverter extends ToSliceDatasetConversion[Sequence, Sequence, SequenceDataset]

125. #### final class SequencesToVariantContextsConverter extends Function2[SequenceDataset, RDD[VariantContext], VariantContextDataset]

126. #### final class SequencesToVariantsConverter extends Function2[SequenceDataset, RDD[Variant], VariantDataset]

127. #### final class SequencesToVariantsDatasetConverter extends ToVariantDatasetConversion[Sequence, Sequence, SequenceDataset]

128. #### final class SlicesToAlignmentsConverter extends Function2[SliceDataset, RDD[Alignment], AlignmentDataset]

129. #### final class SlicesToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Slice, Slice, SliceDataset]

130. #### final class SlicesToCoverageConverter extends Function2[SliceDataset, RDD[Coverage], CoverageDataset]

131. #### final class SlicesToCoverageDatasetConverter extends ToCoverageDatasetConversion[Slice, Slice, SliceDataset]

132. #### final class SlicesToFeaturesConverter extends Function2[SliceDataset, RDD[Feature], FeatureDataset]

133. #### final class SlicesToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Slice, Slice, SliceDataset]

134. #### final class SlicesToFragmentsConverter extends Function2[SliceDataset, RDD[Fragment], FragmentDataset]

135. #### final class SlicesToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Slice, Slice, SliceDataset]

136. #### final class SlicesToGenotypesConverter extends Function2[SliceDataset, RDD[Genotype], GenotypeDataset]

137. #### final class SlicesToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Slice, Slice, SliceDataset]

138. #### final class SlicesToReadsConverter extends Function2[SliceDataset, RDD[Read], ReadDataset]

139. #### final class SlicesToReadsDatasetConverter extends ToReadDatasetConversion[Slice, Slice, SliceDataset]

140. #### final class SlicesToSequencesConverter extends Function2[SliceDataset, RDD[Sequence], SequenceDataset]

141. #### final class SlicesToSequencesDatasetConverter extends ToSequenceDatasetConversion[Slice, Slice, SliceDataset]

142. #### final class SlicesToSlicesConverter extends Function2[SliceDataset, RDD[Slice], SliceDataset]

143. #### final class SlicesToVariantContextsConverter extends Function2[SliceDataset, RDD[VariantContext], VariantContextDataset]

144. #### final class SlicesToVariantsConverter extends Function2[SliceDataset, RDD[Variant], VariantDataset]

145. #### final class SlicesToVariantsDatasetConverter extends ToVariantDatasetConversion[Slice, Slice, SliceDataset]

146. #### trait ToAlignmentDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Alignment, Alignment, AlignmentDataset]

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

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

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

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

151. #### trait ToReadDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Read, Read, ReadDataset]

152. #### trait ToSequenceDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Sequence, Sequence, SequenceDataset]

153. #### trait ToSliceDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Slice, Slice, SliceDataset]

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

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

156. #### final class VariantContextsToAlignmentsConverter extends Function2[VariantContextDataset, RDD[Alignment], AlignmentDataset]

157. #### final class VariantContextsToCoverageConverter extends Function2[VariantContextDataset, RDD[Coverage], CoverageDataset]

158. #### final class VariantContextsToFeaturesConverter extends Function2[VariantContextDataset, RDD[Feature], FeatureDataset]

159. #### final class VariantContextsToFragmentsConverter extends Function2[VariantContextDataset, RDD[Fragment], FragmentDataset]

160. #### final class VariantContextsToGenotypesConverter extends Function2[VariantContextDataset, RDD[Genotype], GenotypeDataset]

161. #### final class VariantContextsToReadsConverter extends Function2[VariantContextDataset, RDD[Read], ReadDataset]

162. #### final class VariantContextsToSequencesConverter extends Function2[VariantContextDataset, RDD[Sequence], SequenceDataset]

163. #### final class VariantContextsToSlicesConverter extends Function2[VariantContextDataset, RDD[Slice], SliceDataset]

164. #### final class VariantContextsToVariantContextConverter extends Function2[VariantContextDataset, RDD[VariantContext], VariantContextDataset]

165. #### final class VariantContextsToVariantsConverter extends Function2[VariantContextDataset, RDD[Variant], VariantDataset]

166. #### final class VariantsToAlignmentsConverter extends Function2[VariantDataset, RDD[Alignment], AlignmentDataset]

167. #### final class VariantsToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Variant, Variant, VariantDataset]

168. #### final class VariantsToCoverageConverter extends Function2[VariantDataset, RDD[Coverage], CoverageDataset]

169. #### final class VariantsToCoverageDatasetConverter extends ToCoverageDatasetConversion[Variant, Variant, VariantDataset]

170. #### final class VariantsToFeaturesConverter extends Function2[VariantDataset, RDD[Feature], FeatureDataset]

171. #### final class VariantsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Variant, Variant, VariantDataset]

172. #### final class VariantsToFragmentsConverter extends Function2[VariantDataset, RDD[Fragment], FragmentDataset]

173. #### final class VariantsToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Variant, Variant, VariantDataset]

174. #### final class VariantsToGenotypesConverter extends Function2[VariantDataset, RDD[Genotype], GenotypeDataset]

175. #### final class VariantsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Variant, Variant, VariantDataset]

176. #### final class VariantsToReadsConverter extends Function2[VariantDataset, RDD[Read], ReadDataset]

177. #### final class VariantsToReadsDatasetConverter extends ToReadDatasetConversion[Variant, Variant, VariantDataset]

178. #### final class VariantsToSequencesConverter extends Function2[VariantDataset, RDD[Sequence], SequenceDataset]

179. #### final class VariantsToSequencesDatasetConverter extends ToSequenceDatasetConversion[Variant, Variant, VariantDataset]

180. #### final class VariantsToSlicesConverter extends Function2[VariantDataset, RDD[Slice], SliceDataset]

181. #### final class VariantsToSlicesDatasetConverter extends ToSliceDatasetConversion[Variant, Variant, VariantDataset]

182. #### final class VariantsToVariantContextConverter extends Function2[VariantDataset, RDD[VariantContext], VariantContextDataset]

183. #### final class VariantsToVariantsConverter extends Function2[VariantDataset, RDD[Variant], VariantDataset]

### Value Members

1. #### object JavaADAMContext extends Serializable

### Ungrouped