ADAMBAMOutputFormat
read
ADAMBAMOutputFormatHeaderLess
read
ADAMCRAMOutputFormat
read
ADAMCRAMOutputFormatHeaderLess
read
ADAMContext
rdd
ADAMHeaderlessVCFOutputFormat
variant
ADAMKryoRegistrator
serialization
ADAMSAMOutputFormat
read
ADAMSAMOutputFormatHeaderLess
read
ADAMSaveAnyArgs
rdd
ADAMVCFOutputFormat
variant
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
adam
bdgenomics
aggregatedCoverage
CoverageRDD
algorithms
adam
aliases
FeatureField
alignments
FragmentField
all
ReferenceRegion
allHeaderLines
DefaultHeaderLines
alleleCount
DefaultHeaderLines
VariantAnnotationField
alleleFrequency
DefaultHeaderLines
VariantAnnotationField
alleles
GenotypeField
allelicDepth
DefaultHeaderLines
alphabet
ReadField
SequenceField
SliceField
alternateAllele
TranscriptEffectField
VariantField
alternateReadDepth
GenotypeField
ancestralAllele
DefaultHeaderLines
VariantAnnotationField
apply
Alphabet
MdTag
RecordGroup
RecordGroupDictionary
ReferencePosition
ReferenceRegion
SequenceDictionary
SequenceRecord
SnpTable
VariantContext
Filter
Projection
GenomicPositionPartitioner
GenomicRegionPartitioner
InFormatterCompanion
BEDInFormatter
GFF3InFormatter
GTFInFormatter
NarrowPeakInFormatter
InterleavedFASTQInFormatter
AnySAMInFormatterCompanion
VCFInFormatter
ReferenceContigMap
arrayRegex
AttributeUtils
asSingleFile
ADAMSaveAnyArgs
assembly
SequenceRecord
ContigField
attrRegex
AttributeUtils
attributes
AlignmentRecordField
FeatureField
SampleField
VariantAnnotationField
VariantCallingAnnotationsField