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org
org.bdgenomics
org.bdgenomics.adam
org.bdgenomics.adam.algorithms
org.bdgenomics.adam.algorithms.smithwaterman
(trait)
SmithWaterman
(case class)
SmithWatermanConstantGapScoring
org.bdgenomics.adam.converters
(class)
AlignmentRecordConverter
(object)
VariantAnnotations
org.bdgenomics.adam.instrumentation
(object)
Timers
org.bdgenomics.adam.io
(class)
InterleavedFastqInputFormat
(class)
SingleFastqInputFormat
org.bdgenomics.adam.models
(object)
(trait)
Alphabet
(case class)
Attribute
(object)
(case class)
Coverage
(class)
DNAAlphabet
(object)
(class)
MultiContigNonoverlappingRegions
(object)
(class)
NonoverlappingRegions
(object)
OptionalPositionOrdering
(trait)
OptionalReferenceOrdering
(object)
OptionalRegionOrdering
(object)
PositionOrdering
(object)
(case class)
ProgramRecord
(object)
(case class)
ReadBucket
(class)
ReadBucketSerializer
(object)
(case class)
RecordGroup
(object)
(case class)
RecordGroupDictionary
(trait)
ReferenceOrdering
(object)
(class)
ReferencePosition
(object)
(case class)
ReferencePositionPair
(class)
ReferencePositionPairSerializer
(class)
ReferencePositionSerializer
(object)
(case class)
ReferenceRegion
(class)
ReferenceRegionSerializer
(object)
RegionOrdering
(class)
SAMFileHeaderWritable
(object)
(class)
SequenceDictionary
(object)
SequenceOrderingByName
(object)
SequenceOrderingByRefIdx
(object)
(case class)
SequenceRecord
(object)
(case class)
SingleReadBucket
(class)
SingleReadBucketSerializer
(object)
(class)
SnpTable
(case class)
Symbol
(object)
TagType
(object)
(class)
VariantContext
(case class)
VCFHeaderWritable
org.bdgenomics.adam.projections
(object)
AlignmentRecordField
(object)
DatabaseVariantAnnotationField
(object)
DbxrefField
(object)
FeatureField
(class)
FieldEnumeration
(trait)
FieldValue
(object)
Filter
(object)
GenotypeField
(object)
NucleotideContigFragmentField
(object)
OntologyTermField
(object)
Projection
(object)
VariantCallingAnnotationsField
(object)
VariantField
org.bdgenomics.adam.rdd
(object)
(class)
ADAMContext
(trait)
ADAMSaveAnyArgs
(class)
AvroGenomicRDD
(class)
AvroReadGroupGenomicRDD
(trait)
BroadcastRegionJoin
(object)
FileMerger
(case class)
FullOuterShuffleRegionJoin
(case class)
GenomeBins
(object)
(case class)
GenomicPositionPartitioner
(trait)
GenomicRDD
(object)
(case class)
GenomicRegionPartitioner
(trait)
InFormatter
(trait)
InFormatterCompanion
(case class)
InnerBroadcastRegionJoin
(case class)
InnerShuffleRegionJoin
(case class)
InnerShuffleRegionJoinAndGroupByLeft
(case class)
LeftOuterShuffleRegionJoin
(class)
MultisampleAvroGenomicRDD
(trait)
MultisampleGenomicRDD
(trait)
OutFormatter
(case class)
ReferencePartitioner
(trait)
RegionJoin
(case class)
RightOuterBroadcastRegionJoin
(case class)
RightOuterShuffleRegionJoin
(case class)
RightOuterShuffleRegionJoinAndGroupByLeft
(trait)
ShuffleRegionJoin
(trait)
Unaligned
org.bdgenomics.adam.rdd.contig
(object)
(case class)
NucleotideContigFragmentRDD
org.bdgenomics.adam.rdd.features
(case class)
CoverageRDD
(object)
(case class)
FeatureRDD
org.bdgenomics.adam.rdd.fragment
(case class)
FragmentRDD
(object)
(class)
InterleavedFASTQInFormatter
org.bdgenomics.adam.rdd.read
(class)
ADAMBAMOutputFormat
(class)
ADAMBAMOutputFormatHeaderLess
(class)
ADAMCRAMOutputFormat
(class)
ADAMCRAMOutputFormatHeaderLess
(class)
ADAMSAMOutputFormat
(class)
ADAMSAMOutputFormatHeaderLess
(case class)
AlignedReadRDD
(trait)
AlignmentRecordRDD
(trait)
AnySAMInFormatter
(trait)
AnySAMInFormatterCompanion
(class)
AnySAMOutFormatter
(object)
(case class)
BAMInFormatter
(object)
(case class)
DuplicateMetrics
(object)
FlagStat
(object)
(case class)
FlagStatMetrics
(case class)
IncorrectMDTagException
(class)
InstrumentedADAMBAMOutputFormat
(class)
InstrumentedADAMBAMOutputFormatHeaderLess
(class)
InstrumentedADAMCRAMOutputFormat
(class)
InstrumentedADAMCRAMOutputFormatHeaderLess
(class)
InstrumentedADAMSAMOutputFormat
(class)
InstrumentedADAMSAMOutputFormatHeaderLess
(object)
(case class)
MDTagging
(object)
(case class)
SAMInFormatter
(object)
(case class)
UnalignedReadRDD
org.bdgenomics.adam.rdd.read.realignment
(object)
(class)
IndelRealignmentTarget
(class)
IndelRealignmentTargetSerializer
(object)
(class)
RealignmentTargetFinder
(object)
TargetOrdering
(object)
(case class)
TargetSet
(class)
TargetSetSerializer
(object)
ZippedTargetOrdering
(case class)
ZippedTargetSet
(class)
ZippedTargetSetSerializer
org.bdgenomics.adam.rdd.read.recalibration
(class)
AbstractCovariate
(object)
(class)
Aggregate
(object)
(class)
BaseQualityRecalibration
(trait)
Covariate
(class)
CovariateKey
(object)
(class)
CovariateSpace
(class)
CycleCovariate
(class)
DinucCovariate
(class)
ExtrasTables
(object)
(class)
Observation
(object)
(class)
ObservationAccumulator
(class)
ObservationTable
(class)
QualityTable
(object)
(class)
RecalibrationTable
(object)
(class)
Recalibrator
org.bdgenomics.adam.rdd.variation
(class)
ADAMHeaderlessVCFOutputFormat
(class)
ADAMVCFOutputFormat
(case class)
DatabaseVariantAnnotationRDD
(case class)
GenotypeRDD
(case class)
VariantContextRDD
(case class)
VariantRDD
(object)
(case class)
VCFInFormatter
(case class)
VCFOutFormatter
org.bdgenomics.adam.rich
(class)
IlluminaOptics
(case class)
ReferenceSequenceContext
(object)
(class)
RichAlignmentRecord
(object)
(class)
RichCigar
(object)
(class)
RichGenotype
(object)
(class)
RichVariant
org.bdgenomics.adam.serialization
(class)
ADAMKryoRegistrator
(class)
AvroSerializer
(case class)
InputStreamWithDecoder
org.bdgenomics.adam.util
(object)
AttributeUtils
(object)
Flattener
(object)
ImplicitJavaConversions
(class)
IntervalListReader
(object)
MapTools
(object)
(class)
MdTag
(object)
MdTagEvent
(class)
ParquetFileTraversable
(object)
ParquetLogger
(object)
PhredUtils
(object)
(class)
QualityScore
(object)
(case class)
ReferenceContigMap
(trait)
ReferenceFile
(object)
(class)
RegExp
(object)
(class)
TwoBitFile
(class)
TwoBitFileSerializer
(object)
Util