ADAMBAMOutputFormat
read
ADAMBAMOutputFormatHeaderLess
read
ADAMCRAMOutputFormat
read
ADAMCRAMOutputFormatHeaderLess
read
ADAMContext
rdd
ADAMContextFromSession
ADAMContext
ADAMKryoRegistrator
serialization
ADAMSAMOutputFormat
read
ADAMSAMOutputFormatHeaderLess
read
ADAMSaveAnyArgs
rdd
ADAMShell
util
ADAMVCFOutputFormat
variant
AlignmentRecord
sql
AlignmentRecordConverter
converters
AlignmentRecordDataset
read
AlignmentRecordField
projections
Alphabet
models
AnySAMInFormatter
read
AnySAMInFormatterCompanion
read
AnySAMOutFormatter
read
Attribute
models
AttributeUtils
util
AvroGenomicDataset
rdd
AvroReadGroupGenomicDataset
rdd
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
alignmentRecordsToAlignmentRecordsConversionFn
ADAMContext
alignmentRecordsToContigsConversionFn
ADAMContext
alignmentRecordsToContigsDatasetConversionFn
ADAMContext
alignmentRecordsToCoverageConversionFn
ADAMContext
alignmentRecordsToCoverageDatasetConversionFn
ADAMContext
alignmentRecordsToFeaturesConversionFn
ADAMContext
alignmentRecordsToFeaturesDatasetConversionFn
ADAMContext
alignmentRecordsToFragmentsConversionFn
ADAMContext
alignmentRecordsToFragmentsDatasetConversionFn
ADAMContext
alignmentRecordsToGenotypesConversionFn
ADAMContext
alignmentRecordsToGenotypesDatasetConversionFn
ADAMContext
alignmentRecordsToVariantContextConversionFn
ADAMContext
alignmentRecordsToVariantsConversionFn
ADAMContext
alignmentRecordsToVariantsDatasetConversionFn
ADAMContext
alignments
FragmentField Fragment
all
ReferenceRegion
allHeaderLines
DefaultHeaderLines
alleleCount
DefaultHeaderLines VariantAnnotationField VariantAnnotation
alleleFrequency
DefaultHeaderLines VariantAnnotationField VariantAnnotation
alleles
GenotypeField Genotype
allelicDepth
DefaultHeaderLines
alphabet
ReadField SequenceField SliceField
alternateAllele
TranscriptEffectField VariantField TranscriptEffect Variant
alternateReadDepth
GenotypeField Genotype
ancestralAllele
DefaultHeaderLines VariantAnnotationField VariantAnnotation
annotation
VariantField Variant
apply
VariantContextConverter Alphabet MdTag ReadGroup ReadGroupDictionary ReferencePosition ReferenceRegion SequenceDictionary SequenceRecord SnpTable VariantContext Filter Projection GenomicPositionPartitioner GenomicRegionPartitioner InFormatterCompanion NucleotideContigFragmentDataset BEDInFormatter CoverageDataset FeatureDataset GFF3InFormatter GTFInFormatter NarrowPeakInFormatter FragmentDataset InterleavedFASTQInFormatter Tab5InFormatter Tab6InFormatter AlignmentRecordDataset AnySAMInFormatterCompanion FASTQInFormatter QualityScoreBin GenotypeDataset VCFInFormatter VariantContextDataset VariantDataset GenomeFileReader ReferenceContigMap SequenceDictionaryReader
arrayRegex
AttributeUtils
asSingleFile
ADAMSaveAnyArgs
assembly
SequenceRecord ReferenceField Reference
attrRegex
AttributeUtils
attributes
AlignmentRecordField FeatureField ReadField SampleField SequenceField SliceField VariantAnnotationField VariantCallingAnnotationsField AlignmentRecord Feature VariantAnnotation VariantCallingAnnotations