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.
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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
- implicit def alignmentRecordsToAlignmentRecordsConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
- implicit def alignmentRecordsToContigsConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def alignmentRecordsToContigsDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def alignmentRecordsToCoverageConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Coverage]): CoverageDataset
- implicit def alignmentRecordsToCoverageDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Coverage]): CoverageDataset
- implicit def alignmentRecordsToFeaturesConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Feature]): FeatureDataset
- implicit def alignmentRecordsToFeaturesDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Feature]): FeatureDataset
- implicit def alignmentRecordsToFragmentsConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Fragment]): FragmentDataset
- implicit def alignmentRecordsToFragmentsDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Fragment]): FragmentDataset
- implicit def alignmentRecordsToGenotypesConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Genotype]): GenotypeDataset
- implicit def alignmentRecordsToGenotypesDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Genotype]): GenotypeDataset
- implicit def alignmentRecordsToVariantContextConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[VariantContext]): VariantContextDataset
- implicit def alignmentRecordsToVariantsConversionFn(gDataset: AlignmentRecordDataset, rdd: RDD[Variant]): VariantDataset
- implicit def alignmentRecordsToVariantsDatasetConversionFn(gDataset: AlignmentRecordDataset, ds: Dataset[Variant]): VariantDataset
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- implicit def contigsToAlignmentRecordsConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
- implicit def contigsToAlignmentRecordsDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset
- implicit def contigsToContigsConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def contigsToCoverageConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Coverage]): CoverageDataset
- implicit def contigsToCoverageDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Coverage]): CoverageDataset
- implicit def contigsToFeaturesConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Feature]): FeatureDataset
- implicit def contigsToFeaturesDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Feature]): FeatureDataset
- implicit def contigsToFragmentsConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Fragment]): FragmentDataset
- implicit def contigsToFragmentsDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Fragment]): FragmentDataset
- implicit def contigsToGenotypesConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Genotype]): GenotypeDataset
- implicit def contigsToGenotypesDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Genotype]): GenotypeDataset
- implicit def contigsToVariantContextConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[VariantContext]): VariantContextDataset
- implicit def contigsToVariantsConversionFn(gDataset: NucleotideContigFragmentDataset, rdd: RDD[Variant]): VariantDataset
- implicit def contigsToVariantsDatasetConversionFn(gDataset: NucleotideContigFragmentDataset, ds: Dataset[Variant]): VariantDataset
- implicit def coverageToAlignmentRecordsConversionFn(gDataset: CoverageDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
- implicit def coverageToAlignmentRecordsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset
- implicit def coverageToContigsConversionFn(gDataset: CoverageDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def coverageToContigsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def coverageToCoverageConversionFn(gDataset: CoverageDataset, rdd: RDD[Coverage]): CoverageDataset
- implicit def coverageToFeaturesConversionFn(gDataset: CoverageDataset, rdd: RDD[Feature]): FeatureDataset
- implicit def coverageToFeaturesDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Feature]): FeatureDataset
- implicit def coverageToFragmentsConversionFn(gDataset: CoverageDataset, rdd: RDD[Fragment]): FragmentDataset
- implicit def coverageToFragmentsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Fragment]): FragmentDataset
- implicit def coverageToGenotypesConversionFn(gDataset: CoverageDataset, rdd: RDD[Genotype]): GenotypeDataset
- implicit def coverageToGenotypesDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Genotype]): GenotypeDataset
- implicit def coverageToVariantContextConversionFn(gDataset: CoverageDataset, rdd: RDD[VariantContext]): VariantContextDataset
- implicit def coverageToVariantsConversionFn(gDataset: CoverageDataset, rdd: RDD[Variant]): VariantDataset
- implicit def coverageToVariantsDatasetConversionFn(gDataset: CoverageDataset, ds: Dataset[Variant]): VariantDataset
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- implicit def featuresToAlignmentRecordsConversionFn(gDataset: FeatureDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
- implicit def featuresToAlignmentRecordsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset
- implicit def featuresToContigsConversionFn(gDataset: FeatureDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def featuresToContigsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def featuresToCoverageConversionFn(gDataset: FeatureDataset, rdd: RDD[Coverage]): CoverageDataset
- implicit def featuresToCoverageDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Coverage]): CoverageDataset
- implicit def featuresToFeaturesConversionFn(gDataset: FeatureDataset, rdd: RDD[Feature]): FeatureDataset
- implicit def featuresToFragmentsConversionFn(gDataset: FeatureDataset, rdd: RDD[Fragment]): FragmentDataset
- implicit def featuresToFragmentsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Fragment]): FragmentDataset
- implicit def featuresToGenotypesConversionFn(gDataset: FeatureDataset, rdd: RDD[Genotype]): GenotypeDataset
- implicit def featuresToGenotypesDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Genotype]): GenotypeDataset
- implicit def featuresToVariantContextConversionFn(gDataset: FeatureDataset, rdd: RDD[VariantContext]): VariantContextDataset
- implicit def featuresToVariantsConversionFn(gDataset: FeatureDataset, rdd: RDD[Variant]): VariantDataset
- implicit def featuresToVariantsDatasetConversionFn(gDataset: FeatureDataset, ds: Dataset[Variant]): VariantDataset
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- implicit def fragmentsToAlignmentRecordsConversionFn(gDataset: FragmentDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
- implicit def fragmentsToAlignmentRecordsDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset
- implicit def fragmentsToContigsConversionFn(gDataset: FragmentDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def fragmentsToContigsDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def fragmentsToCoverageConversionFn(gDataset: FragmentDataset, rdd: RDD[Coverage]): CoverageDataset
- implicit def fragmentsToCoverageDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Coverage]): CoverageDataset
- implicit def fragmentsToFeaturesConversionFn(gDataset: FragmentDataset, rdd: RDD[Feature]): FeatureDataset
- implicit def fragmentsToFeaturesDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Feature]): FeatureDataset
- implicit def fragmentsToFragmentsConversionFn(gDataset: FragmentDataset, rdd: RDD[Fragment]): FragmentDataset
- implicit def fragmentsToGenotypesConversionFn(gDataset: FragmentDataset, rdd: RDD[Genotype]): GenotypeDataset
- implicit def fragmentsToGenotypesDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Genotype]): GenotypeDataset
- implicit def fragmentsToVariantContextConversionFn(gDataset: FragmentDataset, rdd: RDD[VariantContext]): VariantContextDataset
- implicit def fragmentsToVariantsConversionFn(gDataset: FragmentDataset, rdd: RDD[Variant]): VariantDataset
- implicit def fragmentsToVariantsDatasetConversionFn(gDataset: FragmentDataset, ds: Dataset[Variant]): VariantDataset
- implicit def genericToAlignmentRecordsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
- implicit def genericToContigsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def genericToCoverageConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Coverage]): CoverageDataset
- implicit def genericToFeatureConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Feature]): FeatureDataset
- implicit def genericToFragmentsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Fragment]): FragmentDataset
- implicit def genericToGenotypesConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Genotype]): GenotypeDataset
- implicit def genericToVariantContextsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[VariantContext]): VariantContextDataset
- implicit def genericToVariantsConversionFn[Y <: GenericGenomicDataset[_, _]](gDataset: Y, rdd: RDD[Variant]): VariantDataset
- implicit def genotypesToAlignmentRecordsConversionFn(gDataset: GenotypeDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
- implicit def genotypesToAlignmentRecordsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset
- implicit def genotypesToContigsConversionFn(gDataset: GenotypeDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def genotypesToContigsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def genotypesToCoverageConversionFn(gDataset: GenotypeDataset, rdd: RDD[Coverage]): CoverageDataset
- implicit def genotypesToCoverageDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Coverage]): CoverageDataset
- implicit def genotypesToFeaturesConversionFn(gDataset: GenotypeDataset, rdd: RDD[Feature]): FeatureDataset
- implicit def genotypesToFeaturesDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Feature]): FeatureDataset
- implicit def genotypesToFragmentsConversionFn(gDataset: GenotypeDataset, rdd: RDD[Fragment]): FragmentDataset
- implicit def genotypesToFragmentsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Fragment]): FragmentDataset
- implicit def genotypesToGenotypesConversionFn(gDataset: GenotypeDataset, rdd: RDD[Genotype]): GenotypeDataset
- implicit def genotypesToVariantContextConversionFn(gDataset: GenotypeDataset, rdd: RDD[VariantContext]): VariantContextDataset
- implicit def genotypesToVariantsConversionFn(gDataset: GenotypeDataset, rdd: RDD[Variant]): VariantDataset
- implicit def genotypesToVariantsDatasetConversionFn(gDataset: GenotypeDataset, ds: Dataset[Variant]): VariantDataset
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- implicit def recordToRichRecord(record: AlignmentRecord): RichAlignmentRecord
- implicit def sparkContextToADAMContext(sc: SparkContext): ADAMContext
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- implicit def variantContextsToAlignmentRecordsConversionFn(gDataset: VariantContextDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
- implicit def variantContextsToContigsConversionFn(gDataset: VariantContextDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def variantContextsToCoverageConversionFn(gDataset: VariantContextDataset, rdd: RDD[Coverage]): CoverageDataset
- implicit def variantContextsToFeaturesConversionFn(gDataset: VariantContextDataset, rdd: RDD[Feature]): FeatureDataset
- implicit def variantContextsToFragmentsConversionFn(gDataset: VariantContextDataset, rdd: RDD[Fragment]): FragmentDataset
- implicit def variantContextsToGenotypesConversionFn(gDataset: VariantContextDataset, rdd: RDD[Genotype]): GenotypeDataset
- implicit def variantContextsToVariantContextsConversionFn(gDataset: VariantContextDataset, rdd: RDD[VariantContext]): VariantContextDataset
- implicit def variantContextsToVariantsConversionFn(gDataset: VariantContextDataset, rdd: RDD[Variant]): VariantDataset
- implicit def variantsToAlignmentRecordsConversionFn(gDataset: VariantDataset, rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
- implicit def variantsToAlignmentRecordsDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[AlignmentRecord]): AlignmentRecordDataset
- implicit def variantsToContigsConversionFn(gDataset: VariantDataset, rdd: RDD[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def variantsToContigsDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[NucleotideContigFragment]): NucleotideContigFragmentDataset
- implicit def variantsToCoverageConversionFn(gDataset: VariantDataset, rdd: RDD[Coverage]): CoverageDataset
- implicit def variantsToCoverageDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Coverage]): CoverageDataset
- implicit def variantsToFeaturesConversionFn(gDataset: VariantDataset, rdd: RDD[Feature]): FeatureDataset
- implicit def variantsToFeaturesDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Feature]): FeatureDataset
- implicit def variantsToFragmentsConversionFn(gDataset: VariantDataset, rdd: RDD[Fragment]): FragmentDataset
- implicit def variantsToFragmentsDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Fragment]): FragmentDataset
- implicit def variantsToGenotypesConversionFn(gDataset: VariantDataset, rdd: RDD[Genotype]): GenotypeDataset
- implicit def variantsToGenotypesDatasetConversionFn(gDataset: VariantDataset, ds: Dataset[Genotype]): GenotypeDataset
- implicit def variantsToVariantContextConversionFn(gDataset: VariantDataset, rdd: RDD[VariantContext]): VariantContextDataset
- implicit def variantsToVariantsConversionFn(gDataset: VariantDataset, rdd: RDD[Variant]): VariantDataset
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