ADAM_2.12: Core 0.35.0 API < Back
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# Packages

-  package root
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-  package org
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-  package bdgenomics
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-  package adam
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    bdgenomics
-  package ds
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    adam
-  package feature
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    ds
-  package fragment
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    ds
-  package read
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    ds
-  package sequence
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    ds
-  package variant
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    ds
- ADAMContext
- ADAMSaveAnyArgs
- AvroGenomicDataset
- AvroReadGroupGenomicDataset
- DatasetBoundGenericGenomicDataset
- DatasetBoundGenomicDataset
- FullOuterShuffleRegionJoin
- GenericConverter
- GenericGenomicDataset
- GenomeBins
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- GenomicDatasetConversion
- GenomicDatasetWithLineage
- GenomicPositionPartitioner
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- InFormatter
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- InnerShuffleRegionJoin
- InnerShuffleRegionJoinAndGroupByLeft
- InnerTreeRegionJoin
- InnerTreeRegionJoinAndGroupByRight
- LeftOuterShuffleRegionJoin
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- MultisampleAvroGenomicDataset
- MultisampleGenomicDataset
- OutFormatter
- RDDBoundGenericGenomicDataset
- ReferencePartitioner
- RegionJoin
- RightOuterShuffleRegionJoinAndGroupByLeft
- RightOuterTreeRegionJoin
- RightOuterTreeRegionJoinAndGroupByRight
- ShuffleRegionJoin
- SortedIntervalPartitionJoinWithVictims
- TreeRegionJoin
- VictimlessSortedIntervalPartitionJoin

o

org.bdgenomics.adam.ds

# 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
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1. ADAMContext
2. Serializable
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### 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.

   ss

     SparkSession

   returns

     ADAMContext

5.  implicit def AlignmentsToAlignmentsConversionFn(gDataset: AlignmentDataset, rdd: RDD[Alignment]): AlignmentDataset
6.  implicit def AlignmentsToCoverageConversionFn(gDataset: AlignmentDataset, rdd: RDD[Coverage]): CoverageDataset
7.  implicit def AlignmentsToCoverageDatasetConversionFn(gDataset: AlignmentDataset, ds: Dataset[Coverage]): CoverageDataset
8.  implicit def AlignmentsToFeaturesConversionFn(gDataset: AlignmentDataset, rdd: RDD[Feature]): FeatureDataset
9.  implicit def AlignmentsToFeaturesDatasetConversionFn(gDataset: AlignmentDataset, ds: Dataset[Feature]): FeatureDataset
10.  implicit def AlignmentsToFragmentsConversionFn(gDataset: AlignmentDataset, rdd: RDD[Fragment]): FragmentDataset
11.  implicit def AlignmentsToFragmentsDatasetConversionFn(gDataset: AlignmentDataset, ds: Dataset[Fragment]): FragmentDataset
12.  implicit def AlignmentsToGenotypesConversionFn(gDataset: AlignmentDataset, rdd: RDD[Genotype]): GenotypeDataset
13.  implicit def AlignmentsToGenotypesDatasetConversionFn(gDataset: AlignmentDataset, ds: Dataset[Genotype]): GenotypeDataset
14.  implicit def AlignmentsToReadsConversionFn(gDataset: AlignmentDataset, rdd: RDD[Read]): ReadDataset
15.  implicit def AlignmentsToReadsDatasetConversionFn(gDataset: AlignmentDataset, ds: Dataset[Read]): ReadDataset
16.  implicit def AlignmentsToSequencesConversionFn(gDataset: AlignmentDataset, rdd: RDD[Sequence]): SequenceDataset
17.  implicit def AlignmentsToSequencesDatasetConversionFn(gDataset: AlignmentDataset, ds: Dataset[Sequence]): SequenceDataset
18.  implicit def AlignmentsToSlicesConversionFn(gDataset: AlignmentDataset, rdd: RDD[Slice]): SliceDataset
19.  implicit def AlignmentsToSlicesDatasetConversionFn(gDataset: AlignmentDataset, ds: Dataset[Slice]): SliceDataset
20.  implicit def AlignmentsToVariantContextConversionFn(gDataset: AlignmentDataset, rdd: RDD[VariantContext]): VariantContextDataset
21.  implicit def AlignmentsToVariantsConversionFn(gDataset: AlignmentDataset, rdd: RDD[Variant]): VariantDataset
22.  implicit def AlignmentsToVariantsDatasetConversionFn(gDataset: AlignmentDataset, ds: Dataset[Variant]): VariantDataset
23.  final def asInstanceOf[T0]: T0
    Definition Classes
      Any
24.  def clone(): AnyRef
    Attributes
      protected[lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native() @HotSpotIntrinsicCandidate()
25.  implicit def coverageToAlignmentsConversionFn(gDataset: CoverageDataset, rdd: RDD[Alignment]): AlignmentDataset
26.  implicit def coverageToAlignmentsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Alignment]): AlignmentDataset
27.  implicit def coverageToCoverageConversionFn(gDataset: CoverageDataset, rdd: RDD[Coverage]): CoverageDataset
28.  implicit def coverageToFeaturesConversionFn(gDataset: CoverageDataset, rdd: RDD[Feature]): FeatureDataset
29.  implicit def coverageToFeaturesDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Feature]): FeatureDataset
30.  implicit def coverageToFragmentsConversionFn(gDataset: CoverageDataset, rdd: RDD[Fragment]): FragmentDataset
31.  implicit def coverageToFragmentsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Fragment]): FragmentDataset
32.  implicit def coverageToGenotypesConversionFn(gDataset: CoverageDataset, rdd: RDD[Genotype]): GenotypeDataset
33.  implicit def coverageToGenotypesDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Genotype]): GenotypeDataset
34.  implicit def coverageToReadsConversionFn(gDataset: CoverageDataset, rdd: RDD[Read]): ReadDataset
35.  implicit def coverageToReadsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Read]): ReadDataset
36.  implicit def coverageToSequencesConversionFn(gDataset: CoverageDataset, rdd: RDD[Sequence]): SequenceDataset
37.  implicit def coverageToSequencesDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Sequence]): SequenceDataset
38.  implicit def coverageToSlicesConversionFn(gDataset: CoverageDataset, rdd: RDD[Slice]): SliceDataset
39.  implicit def coverageToSlicesDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Slice]): SliceDataset
40.  implicit def coverageToVariantContextConversionFn(gDataset: CoverageDataset, rdd: RDD[VariantContext]): VariantContextDataset
41.  implicit def coverageToVariantsConversionFn(gDataset: CoverageDataset, rdd: RDD[Variant]): VariantDataset
42.  implicit def coverageToVariantsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Variant]): VariantDataset
43.  final def eq(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
44.  def equals(arg0: Any): Boolean
    Definition Classes
      AnyRef → Any
45.  implicit def featuresToAlignmentsConversionFn(gDataset: FeatureDataset, rdd: RDD[Alignment]): AlignmentDataset
46.  implicit def featuresToAlignmentsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Alignment]): AlignmentDataset
47.  implicit def featuresToCoverageConversionFn(gDataset: FeatureDataset, rdd: RDD[Coverage]): CoverageDataset
48.  implicit def featuresToCoverageDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Coverage]): CoverageDataset
49.  implicit def featuresToFeaturesConversionFn(gDataset: FeatureDataset, rdd: RDD[Feature]): FeatureDataset
50.  implicit def featuresToFragmentsConversionFn(gDataset: FeatureDataset, rdd: RDD[Fragment]): FragmentDataset
51.  implicit def featuresToFragmentsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Fragment]): FragmentDataset
52.  implicit def featuresToGenotypesConversionFn(gDataset: FeatureDataset, rdd: RDD[Genotype]): GenotypeDataset
53.  implicit def featuresToGenotypesDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Genotype]): GenotypeDataset
54.  implicit def featuresToReadsConversionFn(gDataset: FeatureDataset, rdd: RDD[Read]): ReadDataset
55.  implicit def featuresToReadsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Read]): ReadDataset
56.  implicit def featuresToSequencesConversionFn(gDataset: FeatureDataset, rdd: RDD[Sequence]): SequenceDataset
57.  implicit def featuresToSequencesDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Sequence]): SequenceDataset
58.  implicit def featuresToSlicesConversionFn(gDataset: FeatureDataset, rdd: RDD[Slice]): SliceDataset
59.  implicit def featuresToSlicesDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Slice]): SliceDataset
60.  implicit def featuresToVariantContextConversionFn(gDataset: FeatureDataset, rdd: RDD[VariantContext]): VariantContextDataset
61.  implicit def featuresToVariantsConversionFn(gDataset: FeatureDataset, rdd: RDD[Variant]): VariantDataset
62.  implicit def featuresToVariantsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Variant]): VariantDataset
63.  implicit def fragmentsToAlignmentsConversionFn(gDataset: FragmentDataset, rdd: RDD[Alignment]): AlignmentDataset
64.  implicit def fragmentsToAlignmentsDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Alignment]): AlignmentDataset
65.  implicit def fragmentsToCoverageConversionFn(gDataset: FragmentDataset, rdd: RDD[Coverage]): CoverageDataset
66.  implicit def fragmentsToCoverageDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Coverage]): CoverageDataset
67.  implicit def fragmentsToFeaturesConversionFn(gDataset: FragmentDataset, rdd: RDD[Feature]): FeatureDataset
68.  implicit def fragmentsToFeaturesDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Feature]): FeatureDataset
69.  implicit def fragmentsToFragmentsConversionFn(gDataset: FragmentDataset, rdd: RDD[Fragment]): FragmentDataset
70.  implicit def fragmentsToGenotypesConversionFn(gDataset: FragmentDataset, rdd: RDD[Genotype]): GenotypeDataset
71.  implicit def fragmentsToGenotypesDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Genotype]): GenotypeDataset
72.  implicit def fragmentsToReadsConversionFn(gDataset: FragmentDataset, rdd: RDD[Read]): ReadDataset
73.  implicit def fragmentsToReadsDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Read]): ReadDataset
74.  implicit def fragmentsToSequencesConversionFn(gDataset: FragmentDataset, rdd: RDD[Sequence]): SequenceDataset
75.  implicit def fragmentsToSequencesDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Sequence]): SequenceDataset
76.  implicit def fragmentsToSlicesConversionFn(gDataset: FragmentDataset, rdd: RDD[Slice]): SliceDataset
77.  implicit def fragmentsToSlicesDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Slice]): SliceDataset
78.  implicit def fragmentsToVariantContextConversionFn(gDataset: FragmentDataset, rdd: RDD[VariantContext]): VariantContextDataset
79.  implicit def fragmentsToVariantsConversionFn(gDataset: FragmentDataset, rdd: RDD[Variant]): VariantDataset
80.  implicit def fragmentsToVariantsDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Variant]): VariantDataset
81.  implicit def genericToAlignmentsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Alignment]): AlignmentDataset
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 genericToReadsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Read]): ReadDataset
87.  implicit def genericToSequencesConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Sequence]): SequenceDataset
88.  implicit def genericToSlicesConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Slice]): SliceDataset
89.  implicit def genericToVariantContextsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[VariantContext]): VariantContextDataset
90.  implicit def genericToVariantsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Variant]): VariantDataset
91.  implicit def genotypesToAlignmentsConversionFn(gDataset: GenotypeDataset, rdd: RDD[Alignment]): AlignmentDataset
92.  implicit def genotypesToAlignmentsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Alignment]): AlignmentDataset
93.  implicit def genotypesToCoverageConversionFn(gDataset: GenotypeDataset, rdd: RDD[Coverage]): CoverageDataset
94.  implicit def genotypesToCoverageDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Coverage]): CoverageDataset
95.  implicit def genotypesToFeaturesConversionFn(gDataset: GenotypeDataset, rdd: RDD[Feature]): FeatureDataset
96.  implicit def genotypesToFeaturesDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Feature]): FeatureDataset
97.  implicit def genotypesToFragmentsConversionFn(gDataset: GenotypeDataset, rdd: RDD[Fragment]): FragmentDataset
98.  implicit def genotypesToFragmentsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Fragment]): FragmentDataset
99.  implicit def genotypesToGenotypesConversionFn(gDataset: GenotypeDataset, rdd: RDD[Genotype]): GenotypeDataset
100.  implicit def genotypesToReadsConversionFn(gDataset: GenotypeDataset, rdd: RDD[Read]): ReadDataset
101.  implicit def genotypesToReadsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Read]): ReadDataset
102.  implicit def genotypesToSequencesConversionFn(gDataset: GenotypeDataset, rdd: RDD[Sequence]): SequenceDataset
103.  implicit def genotypesToSequencesDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Sequence]): SequenceDataset
104.  implicit def genotypesToSlicesConversionFn(gDataset: GenotypeDataset, rdd: RDD[Slice]): SliceDataset
105.  implicit def genotypesToSlicesDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Slice]): SliceDataset
106.  implicit def genotypesToVariantContextConversionFn(gDataset: GenotypeDataset, rdd: RDD[VariantContext]): VariantContextDataset
107.  implicit def genotypesToVariantsConversionFn(gDataset: GenotypeDataset, rdd: RDD[Variant]): VariantDataset
108.  implicit def genotypesToVariantsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Variant]): VariantDataset
109.  final def getClass(): Class[_]
     Definition Classes
       AnyRef → Any
     Annotations
       @native() @HotSpotIntrinsicCandidate()
110.  def hashCode(): Int
     Definition Classes
       AnyRef → Any
     Annotations
       @native() @HotSpotIntrinsicCandidate()
111.  final def isInstanceOf[T0]: Boolean
     Definition Classes
       Any
112.  final def ne(arg0: AnyRef): Boolean
     Definition Classes
       AnyRef
113.  final def notify(): Unit
     Definition Classes
       AnyRef
     Annotations
       @native() @HotSpotIntrinsicCandidate()
114.  final def notifyAll(): Unit
     Definition Classes
       AnyRef
     Annotations
       @native() @HotSpotIntrinsicCandidate()
115.  implicit def readsToAlignmentsConversionFn(gDataset: ReadDataset, rdd: RDD[Alignment]): AlignmentDataset
116.  implicit def readsToAlignmentsDatasetConversionFn(gDataset: ReadDataset, ds: Dataset[Alignment]): AlignmentDataset
117.  implicit def readsToCoverageConversionFn(gDataset: ReadDataset, rdd: RDD[Coverage]): CoverageDataset
118.  implicit def readsToCoverageDatasetConversionFn(gDataset: ReadDataset, ds: Dataset[Coverage]): CoverageDataset
119.  implicit def readsToFeaturesConversionFn(gDataset: ReadDataset, rdd: RDD[Feature]): FeatureDataset
120.  implicit def readsToFeaturesDatasetConversionFn(gDataset: ReadDataset, ds: Dataset[Feature]): FeatureDataset
121.  implicit def readsToFragmentsConversionFn(gDataset: ReadDataset, rdd: RDD[Fragment]): FragmentDataset
122.  implicit def readsToFragmentsDatasetConversionFn(gDataset: ReadDataset, ds: Dataset[Fragment]): FragmentDataset
123.  implicit def readsToGenotypesConversionFn(gDataset: ReadDataset, rdd: RDD[Genotype]): GenotypeDataset
124.  implicit def readsToGenotypesDatasetConversionFn(gDataset: ReadDataset, ds: Dataset[Genotype]): GenotypeDataset
125.  implicit def readsToReadsConversionFn(gDataset: ReadDataset, rdd: RDD[Read]): ReadDataset
126.  implicit def readsToSequencesConversionFn(gDataset: ReadDataset, rdd: RDD[Sequence]): SequenceDataset
127.  implicit def readsToSequencesDatasetConversionFn(gDataset: ReadDataset, ds: Dataset[Sequence]): SequenceDataset
128.  implicit def readsToSlicesConversionFn(gDataset: ReadDataset, rdd: RDD[Slice]): SliceDataset
129.  implicit def readsToSlicesDatasetConversionFn(gDataset: ReadDataset, ds: Dataset[Slice]): SliceDataset
130.  implicit def readsToVariantContextsConversionFn(gDataset: ReadDataset, rdd: RDD[VariantContext]): VariantContextDataset
131.  implicit def readsToVariantsConversionFn(gDataset: ReadDataset, rdd: RDD[Variant]): VariantDataset
132.  implicit def readsToVariantsDatasetConversionFn(gDataset: ReadDataset, ds: Dataset[Variant]): VariantDataset
133.  implicit def recordToRichRecord(record: Alignment): RichAlignment
134.  implicit def sequencesToAlignmentsConversionFn(gDataset: SequenceDataset, rdd: RDD[Alignment]): AlignmentDataset
135.  implicit def sequencesToAlignmentsDatasetConversionFn(gDataset: SequenceDataset, ds: Dataset[Alignment]): AlignmentDataset
136.  implicit def sequencesToCoverageConversionFn(gDataset: SequenceDataset, rdd: RDD[Coverage]): CoverageDataset
137.  implicit def sequencesToCoverageDatasetConversionFn(gDataset: SequenceDataset, ds: Dataset[Coverage]): CoverageDataset
138.  implicit def sequencesToFeaturesConversionFn(gDataset: SequenceDataset, rdd: RDD[Feature]): FeatureDataset
139.  implicit def sequencesToFeaturesDatasetConversionFn(gDataset: SequenceDataset, ds: Dataset[Feature]): FeatureDataset
140.  implicit def sequencesToFragmentsConversionFn(gDataset: SequenceDataset, rdd: RDD[Fragment]): FragmentDataset
141.  implicit def sequencesToFragmentsDatasetConversionFn(gDataset: SequenceDataset, ds: Dataset[Fragment]): FragmentDataset
142.  implicit def sequencesToGenotypesConversionFn(gDataset: SequenceDataset, rdd: RDD[Genotype]): GenotypeDataset
143.  implicit def sequencesToGenotypesDatasetConversionFn(gDataset: SequenceDataset, ds: Dataset[Genotype]): GenotypeDataset
144.  implicit def sequencesToReadsConversionFn(gDataset: SequenceDataset, rdd: RDD[Read]): ReadDataset
145.  implicit def sequencesToReadsDatasetConversionFn(gDataset: SequenceDataset, ds: Dataset[Read]): ReadDataset
146.  implicit def sequencesToSequencesConversionFn(gDataset: SequenceDataset, rdd: RDD[Sequence]): SequenceDataset
147.  implicit def sequencesToSlicesConversionFn(gDataset: SequenceDataset, rdd: RDD[Slice]): SliceDataset
148.  implicit def sequencesToSlicesDatasetConversionFn(gDataset: SequenceDataset, ds: Dataset[Slice]): SliceDataset
149.  implicit def sequencesToVariantContextsConversionFn(gDataset: SequenceDataset, rdd: RDD[VariantContext]): VariantContextDataset
150.  implicit def sequencesToVariantsConversionFn(gDataset: SequenceDataset, rdd: RDD[Variant]): VariantDataset
151.  implicit def sequencesToVariantsDatasetConversionFn(gDataset: SequenceDataset, ds: Dataset[Variant]): VariantDataset
152.  implicit def slicesToAlignmentsConversionFn(gDataset: SliceDataset, rdd: RDD[Alignment]): AlignmentDataset
153.  implicit def slicesToAlignmentsDatasetConversionFn(gDataset: SliceDataset, ds: Dataset[Alignment]): AlignmentDataset
154.  implicit def slicesToCoverageConversionFn(gDataset: SliceDataset, rdd: RDD[Coverage]): CoverageDataset
155.  implicit def slicesToCoverageDatasetConversionFn(gDataset: SliceDataset, ds: Dataset[Coverage]): CoverageDataset
156.  implicit def slicesToFeaturesConversionFn(gDataset: SliceDataset, rdd: RDD[Feature]): FeatureDataset
157.  implicit def slicesToFeaturesDatasetConversionFn(gDataset: SliceDataset, ds: Dataset[Feature]): FeatureDataset
158.  implicit def slicesToFragmentsConversionFn(gDataset: SliceDataset, rdd: RDD[Fragment]): FragmentDataset
159.  implicit def slicesToFragmentsDatasetConversionFn(gDataset: SliceDataset, ds: Dataset[Fragment]): FragmentDataset
160.  implicit def slicesToGenotypesConversionFn(gDataset: SliceDataset, rdd: RDD[Genotype]): GenotypeDataset
161.  implicit def slicesToGenotypesDatasetConversionFn(gDataset: SliceDataset, ds: Dataset[Genotype]): GenotypeDataset
162.  implicit def slicesToReadsConversionFn(gDataset: SliceDataset, rdd: RDD[Read]): ReadDataset
163.  implicit def slicesToReadsDatasetConversionFn(gDataset: SliceDataset, ds: Dataset[Read]): ReadDataset
164.  implicit def slicesToSequencesConversionFn(gDataset: SliceDataset, rdd: RDD[Sequence]): SequenceDataset
165.  implicit def slicesToSequencesDatasetConversionFn(gDataset: SliceDataset, ds: Dataset[Sequence]): SequenceDataset
166.  implicit def slicesToSlicesConversionFn(gDataset: SliceDataset, rdd: RDD[Slice]): SliceDataset
167.  implicit def slicesToVariantContextsConversionFn(gDataset: SliceDataset, rdd: RDD[VariantContext]): VariantContextDataset
168.  implicit def slicesToVariantsConversionFn(gDataset: SliceDataset, rdd: RDD[Variant]): VariantDataset
169.  implicit def slicesToVariantsDatasetConversionFn(gDataset: SliceDataset, ds: Dataset[Variant]): VariantDataset
170.  implicit def sparkContextToADAMContext(sc: SparkContext): ADAMContext
171.  final def synchronized[T0](arg0: ⇒ T0): T0
     Definition Classes
       AnyRef
172.  def toString(): String
     Definition Classes
       AnyRef → Any
173.  implicit def variantContextsToAlignmentsConversionFn(gDataset: VariantContextDataset, rdd: RDD[Alignment]): AlignmentDataset
174.  implicit def variantContextsToCoverageConversionFn(gDataset: VariantContextDataset, rdd: RDD[Coverage]): CoverageDataset
175.  implicit def variantContextsToFeaturesConversionFn(gDataset: VariantContextDataset, rdd: RDD[Feature]): FeatureDataset
176.  implicit def variantContextsToFragmentsConversionFn(gDataset: VariantContextDataset, rdd: RDD[Fragment]): FragmentDataset
177.  implicit def variantContextsToGenotypesConversionFn(gDataset: VariantContextDataset, rdd: RDD[Genotype]): GenotypeDataset
178.  implicit def variantContextsToReadsConversionFn(gDataset: VariantContextDataset, rdd: RDD[Read]): ReadDataset
179.  implicit def variantContextsToSequencesConversionFn(gDataset: VariantContextDataset, rdd: RDD[Sequence]): SequenceDataset
180.  implicit def variantContextsToSlicesConversionFn(gDataset: VariantContextDataset, rdd: RDD[Slice]): SliceDataset
181.  implicit def variantContextsToVariantContextsConversionFn(gDataset: VariantContextDataset, rdd: RDD[VariantContext]): VariantContextDataset
182.  implicit def variantContextsToVariantsConversionFn(gDataset: VariantContextDataset, rdd: RDD[Variant]): VariantDataset
183.  implicit def variantsToAlignmentsConversionFn(gDataset: VariantDataset, rdd: RDD[Alignment]): AlignmentDataset
184.  implicit def variantsToAlignmentsDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Alignment]): AlignmentDataset
185.  implicit def variantsToCoverageConversionFn(gDataset: VariantDataset, rdd: RDD[Coverage]): CoverageDataset
186.  implicit def variantsToCoverageDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Coverage]): CoverageDataset
187.  implicit def variantsToFeaturesConversionFn(gDataset: VariantDataset, rdd: RDD[Feature]): FeatureDataset
188.  implicit def variantsToFeaturesDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Feature]): FeatureDataset
189.  implicit def variantsToFragmentsConversionFn(gDataset: VariantDataset, rdd: RDD[Fragment]): FragmentDataset
190.  implicit def variantsToFragmentsDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Fragment]): FragmentDataset
191.  implicit def variantsToGenotypesConversionFn(gDataset: VariantDataset, rdd: RDD[Genotype]): GenotypeDataset
192.  implicit def variantsToGenotypesDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Genotype]): GenotypeDataset
193.  implicit def variantsToReadsConversionFn(gDataset: VariantDataset, rdd: RDD[Read]): ReadDataset
194.  implicit def variantsToReadsDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Read]): ReadDataset
195.  implicit def variantsToSequencesConversionFn(gDataset: VariantDataset, rdd: RDD[Sequence]): SequenceDataset
196.  implicit def variantsToSequencesDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Sequence]): SequenceDataset
197.  implicit def variantsToSlicesConversionFn(gDataset: VariantDataset, rdd: RDD[Slice]): SliceDataset
198.  implicit def variantsToSlicesDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Slice]): SliceDataset
199.  implicit def variantsToVariantContextConversionFn(gDataset: VariantDataset, rdd: RDD[VariantContext]): VariantContextDataset
200.  implicit def variantsToVariantsConversionFn(gDataset: VariantDataset, rdd: RDD[Variant]): VariantDataset
201.  final def wait(arg0: Long, arg1: Int): Unit
     Definition Classes
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       @throws( ... )
202.  final def wait(arg0: Long): Unit
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       @throws( ... ) @native()
203.  final def wait(): Unit
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       @throws( ... )

### Deprecated Value Members

1.  def finalize(): Unit
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     @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
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     (Since version ) see corresponding Javadoc for more information.

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