Packages

package java

Ordering
  1. Alphabetic
Visibility
  1. Public
  2. All

Type Members

  1. final class AlignmentRecordsToAlignmentRecordsConverter extends Function2[AlignmentRecordDataset, RDD[AlignmentRecord], AlignmentRecordDataset]
  2. final class AlignmentRecordsToContigsConverter extends Function2[AlignmentRecordDataset, RDD[NucleotideContigFragment], NucleotideContigFragmentDataset]
  3. final class AlignmentRecordsToContigsDatasetConverter extends ToContigDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordDataset]
  4. final class AlignmentRecordsToCoverageConverter extends Function2[AlignmentRecordDataset, RDD[Coverage], CoverageDataset]
  5. final class AlignmentRecordsToCoverageDatasetConverter extends ToCoverageDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordDataset]
  6. final class AlignmentRecordsToFeaturesConverter extends Function2[AlignmentRecordDataset, RDD[Feature], FeatureDataset]
  7. final class AlignmentRecordsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordDataset]
  8. final class AlignmentRecordsToFragmentsConverter extends Function2[AlignmentRecordDataset, RDD[Fragment], FragmentDataset]
  9. final class AlignmentRecordsToFragmentsDatasetConverter extends ToFragmentDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordDataset]
  10. final class AlignmentRecordsToGenotypesConverter extends Function2[AlignmentRecordDataset, RDD[Genotype], GenotypeDataset]
  11. final class AlignmentRecordsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordDataset]
  12. final class AlignmentRecordsToVariantContextConverter extends Function2[AlignmentRecordDataset, RDD[VariantContext], VariantContextDataset]
  13. final class AlignmentRecordsToVariantsConverter extends Function2[AlignmentRecordDataset, RDD[Variant], VariantDataset]
  14. final class AlignmentRecordsToVariantsDatasetConverter extends ToVariantDatasetConversion[AlignmentRecord, AlignmentRecord, AlignmentRecordDataset]
  15. final class ContigsToAlignmentRecordsConverter extends Function2[NucleotideContigFragmentDataset, RDD[AlignmentRecord], AlignmentRecordDataset]
  16. final class ContigsToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentDataset]
  17. final class ContigsToContigsConverter extends Function2[NucleotideContigFragmentDataset, RDD[NucleotideContigFragment], NucleotideContigFragmentDataset]
  18. final class ContigsToCoverageConverter extends Function2[NucleotideContigFragmentDataset, RDD[Coverage], CoverageDataset]
  19. final class ContigsToCoverageDatasetConverter extends ToCoverageDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentDataset]
  20. final class ContigsToFeaturesConverter extends Function2[NucleotideContigFragmentDataset, RDD[Feature], FeatureDataset]
  21. final class ContigsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentDataset]
  22. final class ContigsToFragmentsConverter extends Function2[NucleotideContigFragmentDataset, RDD[Fragment], FragmentDataset]
  23. final class ContigsToFragmentsDatasetConverter extends ToFragmentDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentDataset]
  24. final class ContigsToGenotypesConverter extends Function2[NucleotideContigFragmentDataset, RDD[Genotype], GenotypeDataset]
  25. final class ContigsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentDataset]
  26. final class ContigsToVariantContextsConverter extends Function2[NucleotideContigFragmentDataset, RDD[VariantContext], VariantContextDataset]
  27. final class ContigsToVariantsConverter extends Function2[NucleotideContigFragmentDataset, RDD[Variant], VariantDataset]
  28. final class ContigsToVariantsDatasetConverter extends ToVariantDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentDataset]
  29. final class CoverageToAlignmentRecordsConverter extends Function2[CoverageDataset, RDD[AlignmentRecord], AlignmentRecordDataset]
  30. final class CoverageToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Coverage, Coverage, CoverageDataset]
  31. final class CoverageToContigsConverter extends Function2[CoverageDataset, RDD[NucleotideContigFragment], NucleotideContigFragmentDataset]
  32. final class CoverageToContigsDatasetConverter extends ToContigDatasetConversion[Coverage, Coverage, CoverageDataset]
  33. final class CoverageToCoverageConverter extends Function2[CoverageDataset, RDD[Coverage], CoverageDataset]
  34. final class CoverageToFeaturesConverter extends Function2[CoverageDataset, RDD[Feature], FeatureDataset]
  35. final class CoverageToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Coverage, Coverage, CoverageDataset]
  36. final class CoverageToFragmentsConverter extends Function2[CoverageDataset, RDD[Fragment], FragmentDataset]
  37. final class CoverageToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Coverage, Coverage, CoverageDataset]
  38. final class CoverageToGenotypesConverter extends Function2[CoverageDataset, RDD[Genotype], GenotypeDataset]
  39. final class CoverageToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Coverage, Coverage, CoverageDataset]
  40. final class CoverageToVariantContextConverter extends Function2[CoverageDataset, RDD[VariantContext], VariantContextDataset]
  41. final class CoverageToVariantsConverter extends Function2[CoverageDataset, RDD[Variant], VariantDataset]
  42. final class CoverageToVariantsDatasetConverter extends ToVariantDatasetConversion[Coverage, Coverage, CoverageDataset]
  43. final class FeaturesToAlignmentRecordsConverter extends Function2[FeatureDataset, RDD[AlignmentRecord], AlignmentRecordDataset]
  44. final class FeaturesToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Feature, Feature, FeatureDataset]
  45. final class FeaturesToContigsConverter extends Function2[FeatureDataset, RDD[NucleotideContigFragment], NucleotideContigFragmentDataset]
  46. final class FeaturesToContigsDatasetConverter extends ToContigDatasetConversion[Feature, Feature, FeatureDataset]
  47. final class FeaturesToCoverageConverter extends Function2[FeatureDataset, RDD[Coverage], CoverageDataset]
  48. final class FeaturesToCoverageDatasetConverter extends ToCoverageDatasetConversion[Feature, Feature, FeatureDataset]
  49. final class FeaturesToFeatureConverter extends Function2[FeatureDataset, RDD[Feature], FeatureDataset]
  50. final class FeaturesToFragmentsConverter extends Function2[FeatureDataset, RDD[Fragment], FragmentDataset]
  51. final class FeaturesToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Feature, Feature, FeatureDataset]
  52. final class FeaturesToGenotypesConverter extends Function2[FeatureDataset, RDD[Genotype], GenotypeDataset]
  53. final class FeaturesToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Feature, Feature, FeatureDataset]
  54. final class FeaturesToVariantContextConverter extends Function2[FeatureDataset, RDD[VariantContext], VariantContextDataset]
  55. final class FeaturesToVariantsConverter extends Function2[FeatureDataset, RDD[Variant], VariantDataset]
  56. final class FeaturesToVariantsDatasetConverter extends ToVariantDatasetConversion[Feature, Feature, FeatureDataset]
  57. final class FragmentsToAlignmentRecordsConverter extends Function2[FragmentDataset, RDD[AlignmentRecord], AlignmentRecordDataset]
  58. final class FragmentsToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Fragment, Fragment, FragmentDataset]
  59. final class FragmentsToContigsConverter extends Function2[FragmentDataset, RDD[NucleotideContigFragment], NucleotideContigFragmentDataset]
  60. final class FragmentsToContigsDatasetConverter extends ToContigDatasetConversion[Fragment, Fragment, FragmentDataset]
  61. final class FragmentsToCoverageConverter extends Function2[FragmentDataset, RDD[Coverage], CoverageDataset]
  62. final class FragmentsToCoverageDatasetConverter extends ToCoverageDatasetConversion[Fragment, Fragment, FragmentDataset]
  63. final class FragmentsToFeaturesConverter extends Function2[FragmentDataset, RDD[Feature], FeatureDataset]
  64. final class FragmentsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Fragment, Fragment, FragmentDataset]
  65. final class FragmentsToFragmentsConverter extends Function2[FragmentDataset, RDD[Fragment], FragmentDataset]
  66. final class FragmentsToGenotypesConverter extends Function2[FragmentDataset, RDD[Genotype], GenotypeDataset]
  67. final class FragmentsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Fragment, Fragment, FragmentDataset]
  68. final class FragmentsToVariantContextConverter extends Function2[FragmentDataset, RDD[VariantContext], VariantContextDataset]
  69. final class FragmentsToVariantsConverter extends Function2[FragmentDataset, RDD[Variant], VariantDataset]
  70. final class FragmentsToVariantsDatasetConverter extends ToVariantDatasetConversion[Fragment, Fragment, FragmentDataset]
  71. final class GenotypesToAlignmentRecordsConverter extends Function2[GenotypeDataset, RDD[AlignmentRecord], AlignmentRecordDataset]
  72. final class GenotypesToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Genotype, Genotype, GenotypeDataset]
  73. final class GenotypesToContigsConverter extends Function2[GenotypeDataset, RDD[NucleotideContigFragment], NucleotideContigFragmentDataset]
  74. final class GenotypesToContigsDatasetConverter extends ToContigDatasetConversion[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 GenotypesToVariantContextConverter extends Function2[GenotypeDataset, RDD[VariantContext], VariantContextDataset]
  83. final class GenotypesToVariantsConverter extends Function2[GenotypeDataset, RDD[Variant], VariantDataset]
  84. final class GenotypesToVariantsDatasetConverter extends ToVariantDatasetConversion[Genotype, Genotype, GenotypeDataset]
  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, AlignmentRecordDataset]
  87. trait ToContigDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentDataset]
  88. trait ToCoverageDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Coverage, Coverage, CoverageDataset]
  89. trait ToFeatureDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Feature, Feature, FeatureDataset]
  90. trait ToFragmentDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Fragment, Fragment, FragmentDataset]
  91. trait ToGenotypeDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Genotype, Genotype, GenotypeDataset]
  92. trait ToVariantContextDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, VariantContext, VariantContext, VariantContextDataset]
  93. trait ToVariantDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Variant, Variant, VariantDataset]
  94. final class VariantContextsToAlignmentRecordsConverter extends Function2[VariantContextDataset, RDD[AlignmentRecord], AlignmentRecordDataset]
  95. final class VariantContextsToContigsConverter extends Function2[VariantContextDataset, RDD[NucleotideContigFragment], NucleotideContigFragmentDataset]
  96. final class VariantContextsToCoverageConverter extends Function2[VariantContextDataset, RDD[Coverage], CoverageDataset]
  97. final class VariantContextsToFeaturesConverter extends Function2[VariantContextDataset, RDD[Feature], FeatureDataset]
  98. final class VariantContextsToFragmentsConverter extends Function2[VariantContextDataset, RDD[Fragment], FragmentDataset]
  99. final class VariantContextsToGenotypesConverter extends Function2[VariantContextDataset, RDD[Genotype], GenotypeDataset]
  100. final class VariantContextsToVariantContextConverter extends Function2[VariantContextDataset, RDD[VariantContext], VariantContextDataset]
  101. final class VariantContextsToVariantsConverter extends Function2[VariantContextDataset, RDD[Variant], VariantDataset]
  102. final class VariantsToAlignmentRecordsConverter extends Function2[VariantDataset, RDD[AlignmentRecord], AlignmentRecordDataset]
  103. final class VariantsToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Variant, Variant, VariantDataset]
  104. final class VariantsToContigsConverter extends Function2[VariantDataset, RDD[NucleotideContigFragment], NucleotideContigFragmentDataset]
  105. final class VariantsToContigsDatasetConverter extends ToContigDatasetConversion[Variant, Variant, VariantDataset]
  106. final class VariantsToCoverageConverter extends Function2[VariantDataset, RDD[Coverage], CoverageDataset]
  107. final class VariantsToCoverageDatasetConverter extends ToCoverageDatasetConversion[Variant, Variant, VariantDataset]
  108. final class VariantsToFeaturesConverter extends Function2[VariantDataset, RDD[Feature], FeatureDataset]
  109. final class VariantsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Variant, Variant, VariantDataset]
  110. final class VariantsToFragmentsConverter extends Function2[VariantDataset, RDD[Fragment], FragmentDataset]
  111. final class VariantsToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Variant, Variant, VariantDataset]
  112. final class VariantsToGenotypesConverter extends Function2[VariantDataset, RDD[Genotype], GenotypeDataset]
  113. final class VariantsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Variant, Variant, VariantDataset]
  114. final class VariantsToVariantContextConverter extends Function2[VariantDataset, RDD[VariantContext], VariantContextDataset]
  115. final class VariantsToVariantsConverter extends Function2[VariantDataset, RDD[Variant], VariantDataset]

Value Members

  1. object JavaADAMContext extends Serializable

Ungrouped