ADAM_2.12: Core 0.27.0 API < Back
 

# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package rdd
  Definition Classes
    adam
-  package contig
  Definition Classes
    rdd
-  package feature
  Definition Classes
    rdd
-  package fragment
  Definition Classes
    rdd
-  package read
  Definition Classes
    rdd
-  package variant
  Definition Classes
    rdd
- ADAMContext
- ADAMSaveAnyArgs
- AvroGenomicDataset
- AvroReadGroupGenomicDataset
- DatasetBoundGenericGenomicDataset
- DatasetBoundGenomicDataset
- FullOuterShuffleRegionJoin
- GenericConverter
- GenericGenomicDataset
- GenomeBins
- GenomicBroadcast
- GenomicDataset
- GenomicDatasetConversion
- GenomicDatasetWithLineage
- GenomicPositionPartitioner
- GenomicRegionPartitioner
- InFormatter
- InFormatterCompanion
- InnerShuffleRegionJoin
- InnerShuffleRegionJoinAndGroupByLeft
- InnerTreeRegionJoin
- InnerTreeRegionJoinAndGroupByRight
- LeftOuterShuffleRegionJoin
- LeftOuterShuffleRegionJoinAndGroupByLeft
- MultisampleAvroGenomicDataset
- MultisampleGenomicDataset
- OutFormatter
- RDDBoundGenericGenomicDataset
- ReferencePartitioner
- RegionJoin
- RightOuterShuffleRegionJoinAndGroupByLeft
- RightOuterTreeRegionJoin
- RightOuterTreeRegionJoinAndGroupByRight
- ShuffleRegionJoin
- SortedIntervalPartitionJoinWithVictims
- TreeRegionJoin
- VictimlessSortedIntervalPartitionJoin

o

org.bdgenomics.adam.rdd

# ADAMContext 

###
Companion class ADAMContext

#### object ADAMContext extends Serializable

This singleton provides an implicit conversion from a SparkContext to the ADAMContext, as well as implicit functions for the Pipe API.

Linear Supertypes
Serializable, Serializable, AnyRef, Any
 
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. ADAMContext
2. Serializable
3. Serializable
4. AnyRef
5. Any

1. Hide All
2. Show All

Visibility

1. Public
2. All

### Value Members

1.  final def !=(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
2.  final def ##(): Int
   Definition Classes
     AnyRef → Any
3.  final def ==(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
4.  def ADAMContextFromSession(ss: SparkSession): ADAMContext

   Creates an ADAMContext from a SparkSession.

   Creates an ADAMContext from a SparkSession. Sets active session, including SQLContext, to input session.

   ss

     SparkSession

   returns

     ADAMContext

5.  implicit def alignmentRecordsToAlignmentRecordsConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
6.  implicit def alignmentRecordsToContigsConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
7.  implicit def alignmentRecordsToContigsDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset
8.  implicit def alignmentRecordsToCoverageConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Coverage]): CoverageDataset
9.  implicit def alignmentRecordsToCoverageDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Coverage]): CoverageDataset
10.  implicit def alignmentRecordsToFeaturesConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Feature]): FeatureDataset
11.  implicit def alignmentRecordsToFeaturesDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Feature]): FeatureDataset
12.  implicit def alignmentRecordsToFragmentsConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Fragment]): FragmentDataset
13.  implicit def alignmentRecordsToFragmentsDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Fragment]): FragmentDataset
14.  implicit def alignmentRecordsToGenotypesConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Genotype]): GenotypeDataset
15.  implicit def alignmentRecordsToGenotypesDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Genotype]): GenotypeDataset
16.  implicit def alignmentRecordsToVariantContextConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[VariantContext]): VariantContextDataset
17.  implicit def alignmentRecordsToVariantsConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Variant]): VariantDataset
18.  implicit def alignmentRecordsToVariantsDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Variant]): VariantDataset
19.  final def asInstanceOf[T0]: T0
    Definition Classes
      Any
20.  def clone(): AnyRef
    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @native() @throws( ... )
21.  implicit def contigsToAlignmentRecordsConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
22.  implicit def contigsToAlignmentRecordsDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset
23.  implicit def contigsToContigsConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
24.  implicit def contigsToCoverageConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Coverage]): CoverageDataset
25.  implicit def contigsToCoverageDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Coverage]): CoverageDataset
26.  implicit def contigsToFeaturesConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Feature]): FeatureDataset
27.  implicit def contigsToFeaturesDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Feature]): FeatureDataset
28.  implicit def contigsToFragmentsConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Fragment]): FragmentDataset
29.  implicit def contigsToFragmentsDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Fragment]): FragmentDataset
30.  implicit def contigsToGenotypesConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Genotype]): GenotypeDataset
31.  implicit def contigsToGenotypesDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Genotype]): GenotypeDataset
32.  implicit def contigsToVariantContextConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[VariantContext]): VariantContextDataset
33.  implicit def contigsToVariantsConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Variant]): VariantDataset
34.  implicit def contigsToVariantsDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Variant]): VariantDataset
35.  implicit def coverageToAlignmentRecordsConversionFn(gDataset: CoverageDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
36.  implicit def coverageToAlignmentRecordsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset
37.  implicit def coverageToContigsConversionFn(gDataset: CoverageDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
38.  implicit def coverageToContigsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset
39.  implicit def coverageToCoverageConversionFn(gDataset: CoverageDataset, rdd: RDD[Coverage]): CoverageDataset
40.  implicit def coverageToFeaturesConversionFn(gDataset: CoverageDataset, rdd: RDD[Feature]): FeatureDataset
41.  implicit def coverageToFeaturesDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Feature]): FeatureDataset
42.  implicit def coverageToFragmentsConversionFn(gDataset: CoverageDataset, rdd: RDD[Fragment]): FragmentDataset
43.  implicit def coverageToFragmentsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Fragment]): FragmentDataset
44.  implicit def coverageToGenotypesConversionFn(gDataset: CoverageDataset, rdd: RDD[Genotype]): GenotypeDataset
45.  implicit def coverageToGenotypesDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Genotype]): GenotypeDataset
46.  implicit def coverageToVariantContextConversionFn(gDataset: CoverageDataset, rdd: RDD[VariantContext]): VariantContextDataset
47.  implicit def coverageToVariantsConversionFn(gDataset: CoverageDataset, rdd: RDD[Variant]): VariantDataset
48.  implicit def coverageToVariantsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Variant]): VariantDataset
49.  final def eq(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
50.  def equals(arg0: Any): Boolean
    Definition Classes
      AnyRef → Any
51.  implicit def featuresToAlignmentRecordsConversionFn(gDataset: FeatureDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
52.  implicit def featuresToAlignmentRecordsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset
53.  implicit def featuresToContigsConversionFn(gDataset: FeatureDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
54.  implicit def featuresToContigsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset
55.  implicit def featuresToCoverageConversionFn(gDataset: FeatureDataset, rdd: RDD[Coverage]): CoverageDataset
56.  implicit def featuresToCoverageDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Coverage]): CoverageDataset
57.  implicit def featuresToFeaturesConversionFn(gDataset: FeatureDataset, rdd: RDD[Feature]): FeatureDataset
58.  implicit def featuresToFragmentsConversionFn(gDataset: FeatureDataset, rdd: RDD[Fragment]): FragmentDataset
59.  implicit def featuresToFragmentsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Fragment]): FragmentDataset
60.  implicit def featuresToGenotypesConversionFn(gDataset: FeatureDataset, rdd: RDD[Genotype]): GenotypeDataset
61.  implicit def featuresToGenotypesDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Genotype]): GenotypeDataset
62.  implicit def featuresToVariantContextConversionFn(gDataset: FeatureDataset, rdd: RDD[VariantContext]): VariantContextDataset
63.  implicit def featuresToVariantsConversionFn(gDataset: FeatureDataset, rdd: RDD[Variant]): VariantDataset
64.  implicit def featuresToVariantsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Variant]): VariantDataset
65.  def finalize(): Unit
    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )
66.  implicit def fragmentsToAlignmentRecordsConversionFn(gDataset: FragmentDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
67.  implicit def fragmentsToAlignmentRecordsDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset
68.  implicit def fragmentsToContigsConversionFn(gDataset: FragmentDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
69.  implicit def fragmentsToContigsDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset
70.  implicit def fragmentsToCoverageConversionFn(gDataset: FragmentDataset, rdd: RDD[Coverage]): CoverageDataset
71.  implicit def fragmentsToCoverageDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Coverage]): CoverageDataset
72.  implicit def fragmentsToFeaturesConversionFn(gDataset: FragmentDataset, rdd: RDD[Feature]): FeatureDataset
73.  implicit def fragmentsToFeaturesDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Feature]): FeatureDataset
74.  implicit def fragmentsToFragmentsConversionFn(gDataset: FragmentDataset, rdd: RDD[Fragment]): FragmentDataset
75.  implicit def fragmentsToGenotypesConversionFn(gDataset: FragmentDataset, rdd: RDD[Genotype]): GenotypeDataset
76.  implicit def fragmentsToGenotypesDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Genotype]): GenotypeDataset
77.  implicit def fragmentsToVariantContextConversionFn(gDataset: FragmentDataset, rdd: RDD[VariantContext]): VariantContextDataset
78.  implicit def fragmentsToVariantsConversionFn(gDataset: FragmentDataset, rdd: RDD[Variant]): VariantDataset
79.  implicit def fragmentsToVariantsDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Variant]): VariantDataset
80.  implicit def genericToAlignmentRecordsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
81.  implicit def genericToContigsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
82.  implicit def genericToCoverageConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Coverage]): CoverageDataset
83.  implicit def genericToFeatureConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Feature]): FeatureDataset
84.  implicit def genericToFragmentsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Fragment]): FragmentDataset
85.  implicit def genericToGenotypesConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Genotype]): GenotypeDataset
86.  implicit def genericToVariantContextsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[VariantContext]): VariantContextDataset
87.  implicit def genericToVariantsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Variant]): VariantDataset
88.  implicit def genotypesToAlignmentRecordsConversionFn(gDataset: GenotypeDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
89.  implicit def genotypesToAlignmentRecordsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset
90.  implicit def genotypesToContigsConversionFn(gDataset: GenotypeDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
91.  implicit def genotypesToContigsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset
92.  implicit def genotypesToCoverageConversionFn(gDataset: GenotypeDataset, rdd: RDD[Coverage]): CoverageDataset
93.  implicit def genotypesToCoverageDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Coverage]): CoverageDataset
94.  implicit def genotypesToFeaturesConversionFn(gDataset: GenotypeDataset, rdd: RDD[Feature]): FeatureDataset
95.  implicit def genotypesToFeaturesDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Feature]): FeatureDataset
96.  implicit def genotypesToFragmentsConversionFn(gDataset: GenotypeDataset, rdd: RDD[Fragment]): FragmentDataset
97.  implicit def genotypesToFragmentsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Fragment]): FragmentDataset
98.  implicit def genotypesToGenotypesConversionFn(gDataset: GenotypeDataset, rdd: RDD[Genotype]): GenotypeDataset
99.  implicit def genotypesToVariantContextConversionFn(gDataset: GenotypeDataset, rdd: RDD[VariantContext]): VariantContextDataset
100.  implicit def genotypesToVariantsConversionFn(gDataset: GenotypeDataset, rdd: RDD[Variant]): VariantDataset
101.  implicit def genotypesToVariantsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Variant]): VariantDataset
102.  final def getClass(): Class[_]
     Definition Classes
       AnyRef → Any
     Annotations
       @native()
103.  def hashCode(): Int
     Definition Classes
       AnyRef → Any
     Annotations
       @native()
104.  final def isInstanceOf[T0]: Boolean
     Definition Classes
       Any
105.  final def ne(arg0: AnyRef): Boolean
     Definition Classes
       AnyRef
106.  final def notify(): Unit
     Definition Classes
       AnyRef
     Annotations
       @native()
107.  final def notifyAll(): Unit
     Definition Classes
       AnyRef
     Annotations
       @native()
108.  implicit def recordToRichRecord(record: AlignmentRecord): RichAlignmentRecord
109.  implicit def sparkContextToADAMContext(sc: SparkContext): ADAMContext
110.  final def synchronized[T0](arg0: ⇒ T0): T0
     Definition Classes
       AnyRef
111.  def toString(): String
     Definition Classes
       AnyRef → Any
112.  implicit def variantContextsToAlignmentRecordsConversionFn(gDataset: VariantContextDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
113.  implicit def variantContextsToContigsConversionFn(gDataset: VariantContextDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
114.  implicit def variantContextsToCoverageConversionFn(gDataset: VariantContextDataset, rdd: RDD[Coverage]): CoverageDataset
115.  implicit def variantContextsToFeaturesConversionFn(gDataset: VariantContextDataset, rdd: RDD[Feature]): FeatureDataset
116.  implicit def variantContextsToFragmentsConversionFn(gDataset: VariantContextDataset, rdd: RDD[Fragment]): FragmentDataset
117.  implicit def variantContextsToGenotypesConversionFn(gDataset: VariantContextDataset, rdd: RDD[Genotype]): GenotypeDataset
118.  implicit def variantContextsToVariantContextsConversionFn(gDataset: VariantContextDataset, rdd: RDD[VariantContext]): VariantContextDataset
119.  implicit def variantContextsToVariantsConversionFn(gDataset: VariantContextDataset, rdd: RDD[Variant]): VariantDataset
120.  implicit def variantsToAlignmentRecordsConversionFn(gDataset: VariantDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
121.  implicit def variantsToAlignmentRecordsDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset
122.  implicit def variantsToContigsConversionFn(gDataset: VariantDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
123.  implicit def variantsToContigsDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset
124.  implicit def variantsToCoverageConversionFn(gDataset: VariantDataset, rdd: RDD[Coverage]): CoverageDataset
125.  implicit def variantsToCoverageDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Coverage]): CoverageDataset
126.  implicit def variantsToFeaturesConversionFn(gDataset: VariantDataset, rdd: RDD[Feature]): FeatureDataset
127.  implicit def variantsToFeaturesDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Feature]): FeatureDataset
128.  implicit def variantsToFragmentsConversionFn(gDataset: VariantDataset, rdd: RDD[Fragment]): FragmentDataset
129.  implicit def variantsToFragmentsDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Fragment]): FragmentDataset
130.  implicit def variantsToGenotypesConversionFn(gDataset: VariantDataset, rdd: RDD[Genotype]): GenotypeDataset
131.  implicit def variantsToGenotypesDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Genotype]): GenotypeDataset
132.  implicit def variantsToVariantContextConversionFn(gDataset: VariantDataset, rdd: RDD[VariantContext]): VariantContextDataset
133.  implicit def variantsToVariantsConversionFn(gDataset: VariantDataset, rdd: RDD[Variant]): VariantDataset
134.  final def wait(): Unit
     Definition Classes
       AnyRef
     Annotations
       @throws( ... )
135.  final def wait(arg0: Long, arg1: Int): Unit
     Definition Classes
       AnyRef
     Annotations
       @throws( ... )
136.  final def wait(arg0: Long): Unit
     Definition Classes
       AnyRef
     Annotations
       @native() @throws( ... )

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped