org.bdgenomics.adam.api

java

package java

Visibility
  1. Public
  2. All

Type Members

  1. final class AlignmentRecordsToAlignmentRecordsConverter extends SameTypeConversion[AlignmentRecord, AlignmentRecordRDD]

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

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

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

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

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

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

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

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

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

  11. final class AlignmentRecordsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[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, AlignmentRecordRDD]

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

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

  17. final class ContigsToContigsConverter extends SameTypeConversion[NucleotideContigFragment, NucleotideContigFragmentRDD]

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

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

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

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

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

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

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

  25. final class ContigsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[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, NucleotideContigFragmentRDD]

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

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

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

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

  33. final class CoverageToCoverageConverter extends SameTypeConversion[Coverage, CoverageRDD]

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

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

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

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

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

  39. final class CoverageToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[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, CoverageRDD]

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

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

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

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

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

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

  49. final class FeaturesToFeatureConverter extends SameTypeConversion[Feature, FeatureRDD]

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

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

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

  53. final class FeaturesToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[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, FeatureRDD]

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

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

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

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

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

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

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

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

  65. final class FragmentsToFragmentConverter extends SameTypeConversion[Fragment, FragmentRDD]

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

  67. final class FragmentsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[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, FragmentRDD]

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

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

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

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

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

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

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

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

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

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

  81. final class GenotypesToGenotypesConverter extends SameTypeConversion[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, GenotypeRDD]

  85. class JavaADAMContext extends Serializable

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

  86. sealed trait SameTypeConversion[T, U <: GenomicRDD[T, U]] extends Function2[U, RDD[T], U]

  87. trait ToAlignmentRecordDatasetConversion[T <: Product, U <: GenomicDataset[_, T, U]] extends GenomicDatasetConversion[T, U, AlignmentRecord, AlignmentRecordRDD]

  88. trait ToContigDatasetConversion[T <: Product, U <: GenomicDataset[_, T, U]] extends GenomicDatasetConversion[T, U, NucleotideContigFragment, NucleotideContigFragmentRDD]

  89. trait ToCoverageDatasetConversion[T <: Product, U <: GenomicDataset[_, T, U]] extends GenomicDatasetConversion[T, U, Coverage, CoverageRDD]

  90. trait ToFeatureDatasetConversion[T <: Product, U <: GenomicDataset[_, T, U]] extends GenomicDatasetConversion[T, U, Feature, FeatureRDD]

  91. trait ToFragmentDatasetConversion[T <: Product, U <: GenomicDataset[_, T, U]] extends GenomicDatasetConversion[T, U, Fragment, FragmentRDD]

  92. trait ToGenotypeDatasetConversion[T <: Product, U <: GenomicDataset[_, T, U]] extends GenomicDatasetConversion[T, U, Genotype, GenotypeRDD]

  93. trait ToVariantDatasetConversion[T <: Product, U <: GenomicDataset[_, T, U]] extends GenomicDatasetConversion[T, U, 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 SameTypeConversion[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, VariantRDD]

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

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

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

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

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

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

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

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

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

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

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

  115. final class VariantsToVariantsConverter extends SameTypeConversion[Variant, VariantRDD]

Value Members

  1. object JavaADAMContext extends Serializable

Ungrouped