Packages

package java

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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