ADAMBAMOutputFormat
read
ADAMBAMOutputFormatHeaderLess
read
ADAMCRAMOutputFormat
read
ADAMCRAMOutputFormatHeaderLess
read
ADAMContext
rdd
ADAMContextFromSession
ADAMContext
ADAMKryoRegistrator
serialization
ADAMSAMOutputFormat
read
ADAMSAMOutputFormatHeaderLess
read
ADAMSaveAnyArgs
rdd
ADAMShell
util
ADAMVCFOutputFormat
variant
Alignment
sql
AlignmentConverter
converters
AlignmentDataset
read
AlignmentField
projections
AlignmentsToAlignmentsConversionFn
ADAMContext
AlignmentsToCoverageConversionFn
ADAMContext
AlignmentsToCoverageDatasetConversionFn
ADAMContext
AlignmentsToFeaturesConversionFn
ADAMContext
AlignmentsToFeaturesDatasetConversionFn
ADAMContext
AlignmentsToFragmentsConversionFn
ADAMContext
AlignmentsToFragmentsDatasetConversionFn
ADAMContext
AlignmentsToGenotypesConversionFn
ADAMContext
AlignmentsToGenotypesDatasetConversionFn
ADAMContext
AlignmentsToReadsConversionFn
ADAMContext
AlignmentsToReadsDatasetConversionFn
ADAMContext
AlignmentsToSequencesConversionFn
ADAMContext
AlignmentsToSequencesDatasetConversionFn
ADAMContext
AlignmentsToSlicesConversionFn
ADAMContext
AlignmentsToSlicesDatasetConversionFn
ADAMContext
AlignmentsToVariantContextConversionFn
ADAMContext
AlignmentsToVariantsConversionFn
ADAMContext
AlignmentsToVariantsDatasetConversionFn
ADAMContext
Alphabet
models
AnySAMInFormatter
read
AnySAMInFormatterCompanion
read
AnySAMOutFormatter
read
Attribute
models
AttributeUtils
util
AvroGenomicDataset
rdd
AvroReadGroupGenomicDataset
rdd
AvroSchemaConverter
avro
AvroSerializer
serialization
abbreviation
TypeVal
accession
DbxrefField OntologyTermField Dbxref OntologyTerm
adam
bdgenomics
addProcessingStep
GenomicDatasetWithLineage
addReadGroup
AvroReadGroupGenomicDataset
addReadGroups
AvroReadGroupGenomicDataset
addSample
MultisampleGenomicDataset
addSamples
MultisampleGenomicDataset
addSequence
GenomicDataset
addSequences
GenomicDataset
advanceCache
ShuffleRegionJoin SortedIntervalPartitionJoinWithVictims VictimlessSortedIntervalPartitionJoin
aggregatedCoverage
CoverageDataset
algorithms
adam
aliases
FeatureField Feature
alignmentHeaders
ADAMShell
alignments
FragmentField Fragment
all
ReferenceRegion
allHeaderLines
DefaultHeaderLines
alleleCount
DefaultHeaderLines VariantAnnotationField VariantAnnotation
alleleFrequency
DefaultHeaderLines VariantAnnotationField VariantAnnotation
alleles
GenotypeField Genotype
allelicDepth
DefaultHeaderLines
alphabet
ReadField SequenceField SliceField Read Sequence Slice
alternateAllele
TranscriptEffectField VariantField TranscriptEffect Variant
alternateReadDepth
GenotypeField Genotype
ancestralAllele
DefaultHeaderLines VariantAnnotationField VariantAnnotation
annotation
VariantField Variant
apache
org
apply
VariantContextConverter Alphabet MdTag ReadGroup ReadGroupDictionary ReferencePosition ReferenceRegion SequenceDictionary SequenceRecord SnpTable VariantContext Filter Projection GenomicPositionPartitioner GenomicRegionPartitioner InFormatterCompanion BEDInFormatter CoverageDataset FeatureDataset GFF3InFormatter GTFInFormatter NarrowPeakInFormatter FragmentDataset InterleavedFASTQInFormatter Tab5InFormatter Tab6InFormatter AlignmentDataset AnySAMInFormatterCompanion FASTQInFormatter QualityScoreBin ReadDataset FASTAInFormatter SequenceDataset SliceDataset GenotypeDataset VCFInFormatter VariantContextDataset VariantDataset GenomeFileReader ReferenceContigMap SequenceDictionaryReader
arrayRegex
AttributeUtils
asSingleFile
ADAMSaveAnyArgs
assembly
SequenceRecord ReferenceField Reference
attrRegex
AttributeUtils
attributes
AlignmentField FeatureField ReadField SampleField SequenceField SliceField VariantAnnotationField VariantCallingAnnotationsField Alignment Feature Read Sequence Slice VariantAnnotation VariantCallingAnnotations
avro
parquet