ADAM_2.12: APIs for Java, Python 0.27.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package api
  Definition Classes
    adam
-  package java
  Definition Classes
    api
- AlignmentRecordsToAlignmentRecordsConverter
- AlignmentRecordsToContigsConverter
- AlignmentRecordsToContigsDatasetConverter
- AlignmentRecordsToCoverageConverter
- AlignmentRecordsToCoverageDatasetConverter
- AlignmentRecordsToFeaturesConverter
- AlignmentRecordsToFeaturesDatasetConverter
- AlignmentRecordsToFragmentsConverter
- AlignmentRecordsToFragmentsDatasetConverter
- AlignmentRecordsToGenotypesConverter
- AlignmentRecordsToGenotypesDatasetConverter
- AlignmentRecordsToVariantContextConverter
- AlignmentRecordsToVariantsConverter
- AlignmentRecordsToVariantsDatasetConverter
- ContigsToAlignmentRecordsConverter
- ContigsToAlignmentRecordsDatasetConverter
- ContigsToContigsConverter
- ContigsToCoverageConverter
- ContigsToCoverageDatasetConverter
- ContigsToFeaturesConverter
- ContigsToFeaturesDatasetConverter
- ContigsToFragmentsConverter
- ContigsToFragmentsDatasetConverter
- ContigsToGenotypesConverter
- ContigsToGenotypesDatasetConverter
- ContigsToVariantContextsConverter
- ContigsToVariantsConverter
- ContigsToVariantsDatasetConverter
- CoverageToAlignmentRecordsConverter
- CoverageToAlignmentRecordsDatasetConverter
- CoverageToContigsConverter
- CoverageToContigsDatasetConverter
- CoverageToCoverageConverter
- CoverageToFeaturesConverter
- CoverageToFeaturesDatasetConverter
- CoverageToFragmentsConverter
- CoverageToFragmentsDatasetConverter
- CoverageToGenotypesConverter
- CoverageToGenotypesDatasetConverter
- CoverageToVariantContextConverter
- CoverageToVariantsConverter
- CoverageToVariantsDatasetConverter
- FeaturesToAlignmentRecordsConverter
- FeaturesToAlignmentRecordsDatasetConverter
- FeaturesToContigsConverter
- FeaturesToContigsDatasetConverter
- FeaturesToCoverageConverter
- FeaturesToCoverageDatasetConverter
- FeaturesToFeatureConverter
- FeaturesToFragmentsConverter
- FeaturesToFragmentsDatasetConverter
- FeaturesToGenotypesConverter
- FeaturesToGenotypesDatasetConverter
- FeaturesToVariantContextConverter
- FeaturesToVariantsConverter
- FeaturesToVariantsDatasetConverter
- FragmentsToAlignmentRecordsConverter
- FragmentsToAlignmentRecordsDatasetConverter
- FragmentsToContigsConverter
- FragmentsToContigsDatasetConverter
- FragmentsToCoverageConverter
- FragmentsToCoverageDatasetConverter
- FragmentsToFeaturesConverter
- FragmentsToFeaturesDatasetConverter
- FragmentsToFragmentsConverter
- FragmentsToGenotypesConverter
- FragmentsToGenotypesDatasetConverter
- FragmentsToVariantContextConverter
- FragmentsToVariantsConverter
- FragmentsToVariantsDatasetConverter
- GenotypesToAlignmentRecordsConverter
- GenotypesToAlignmentRecordsDatasetConverter
- GenotypesToContigsConverter
- GenotypesToContigsDatasetConverter
- GenotypesToCoverageConverter
- GenotypesToCoverageDatasetConverter
- GenotypesToFeaturesConverter
- GenotypesToFeaturesDatasetConverter
- GenotypesToFragmentsConverter
- GenotypesToFragmentsDatasetConverter
- GenotypesToGenotypesConverter
- GenotypesToVariantContextConverter
- GenotypesToVariantsConverter
- GenotypesToVariantsDatasetConverter
- JavaADAMContext
- ToAlignmentRecordDatasetConversion
- ToContigDatasetConversion
- ToCoverageDatasetConversion
- ToFeatureDatasetConversion
- ToFragmentDatasetConversion
- ToGenotypeDatasetConversion
- ToVariantContextDatasetConversion
- ToVariantDatasetConversion
- VariantContextsToAlignmentRecordsConverter
- VariantContextsToContigsConverter
- VariantContextsToCoverageConverter
- VariantContextsToFeaturesConverter
- VariantContextsToFragmentsConverter
- VariantContextsToGenotypesConverter
- VariantContextsToVariantContextConverter
- VariantContextsToVariantsConverter
- VariantsToAlignmentRecordsConverter
- VariantsToAlignmentRecordsDatasetConverter
- VariantsToContigsConverter
- VariantsToContigsDatasetConverter
- VariantsToCoverageConverter
- VariantsToCoverageDatasetConverter
- VariantsToFeaturesConverter
- VariantsToFeaturesDatasetConverter
- VariantsToFragmentsConverter
- VariantsToFragmentsDatasetConverter
- VariantsToGenotypesConverter
- VariantsToGenotypesDatasetConverter
- VariantsToVariantContextConverter
- VariantsToVariantsConverter
-  package python
  Definition Classes
    api

p

org.bdgenomics.adam.api

# java 

#### 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