ADAMBAMOutputFormat
read
ADAMBAMOutputFormatHeaderLess
read
ADAMCRAMOutputFormat
read
ADAMCRAMOutputFormatHeaderLess
read
ADAMContext
rdd
ADAMHeaderlessVCFOutputFormat
variation
ADAMKryoRegistrator
serialization
ADAMSAMOutputFormat
read
ADAMSAMOutputFormatHeaderLess
read
ADAMSaveAnyArgs
rdd
ADAMVCFOutputFormat
variation
AbstractCovariate
recalibration
Aggregate
recalibration
AlignedReadRDD
read
AlignmentRecordConverter
converters
AlignmentRecordField
projections
AlignmentRecordRDD
read
Alphabet
models
AnySAMInFormatter
read
AnySAMInFormatterCompanion
read
AnySAMOutFormatter
read
Attribute
models
AttributeUtils
util
AvroGenomicRDD
rdd
AvroReadGroupGenomicRDD
rdd
AvroSerializer
serialization
abbreviation
TypeVal
accession
DbxrefField OntologyTermField
accum
ObservationAccumulator
adam
bdgenomics
add
MapTools
addMDTagsBroadcast
MDTagging
aggregateObservations
RecalibrationTable
aggregatedCoverage
CoverageRDD
algorithms
adam
aliases
FeatureField
allReads
ReadBucket SingleReadBucket
alleleCountMLE
VariantCallingAnnotationsField
alleleFrequencyMLE
VariantCallingAnnotationsField
alleles
GenotypeField
alternateAminoAcid
DatabaseVariantAnnotationField
alternateReadDepth
GenotypeField
alternating
NonoverlappingRegions
ancestralAllele
DatabaseVariantAnnotationField
apply
Alphabet MultiContigNonoverlappingRegions NonoverlappingRegions ProgramRecord RecordGroup RecordGroupDictionary ReferencePosition ReferencePositionPair ReferenceRegion SequenceDictionary SequenceRecord SingleReadBucket SnpTable VariantContext Filter Projection GenomicPositionPartitioner GenomicRegionPartitioner InFormatterCompanion InterleavedFASTQInFormatter AnySAMInFormatterCompanion DuplicateMetrics FlagStat MDTagging IndelRealignmentTarget RealignmentTargetFinder TargetSet Aggregate BaseQualityRecalibration Covariate CovariateSpace Observation ObservationAccumulator RecalibrationTable Recalibrator VCFInFormatter RichAlignmentRecord RichCigar MdTag QualityScore ReferenceContigMap RegExp
arrayRegex
AttributeUtils
asSingleFile
ADAMSaveAnyArgs
assembly
SequenceRecord
attrRegex
AttributeUtils
attributes
AlignmentRecordField FeatureField