ObservationAccumulatorComb
Timers
ObservationAccumulatorSeq
Timers
ObservingRead
Timers
OntologyTerm
sql
OntologyTermField
projections
OptionalPositionOrdering
models
OptionalReferenceOrdering
models
OptionalRegionOrdering
models
OutFormatter
rdd
ontologyTerms
FeatureField Feature
opt
ReferenceRegion
optHeaderLines
VCFOutFormatter
optLookbackPartitions
DatasetBoundGenomicDataset DatasetBoundNucleotideContigFragmentDataset DatasetBoundCoverageDataset DatasetBoundFeatureDataset DatasetBoundFragmentDataset DatasetBoundAlignmentRecordDataset DatasetBoundGenotypeDataset DatasetBoundVariantContextDataset DatasetBoundVariantDataset
optPartitionBinSize
DatasetBoundGenomicDataset DatasetBoundNucleotideContigFragmentDataset DatasetBoundCoverageDataset DatasetBoundFeatureDataset DatasetBoundFragmentDataset DatasetBoundAlignmentRecordDataset DatasetBoundGenotypeDataset DatasetBoundVariantContextDataset DatasetBoundVariantDataset
optPartitionMap
DatasetBoundGenericGenomicDataset GenomicDataset RDDBoundGenericGenomicDataset DatasetBoundNucleotideContigFragmentDataset ParquetUnboundNucleotideContigFragmentDataset RDDBoundNucleotideContigFragmentDataset DatasetBoundCoverageDataset DatasetBoundFeatureDataset ParquetUnboundCoverageDataset ParquetUnboundFeatureDataset RDDBoundCoverageDataset RDDBoundFeatureDataset DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset DatasetBoundAlignmentRecordDataset ParquetUnboundAlignmentRecordDataset RDDBoundAlignmentRecordDataset DatasetBoundGenotypeDataset DatasetBoundVariantContextDataset DatasetBoundVariantDataset ParquetUnboundGenotypeDataset ParquetUnboundVariantDataset RDDBoundGenotypeDataset RDDBoundVariantContextDataset RDDBoundVariantDataset
optSampleId
Coverage
orderingForOptionalPositions
ReferencePosition ReferenceRegion
orderingForPositions
ReferencePosition ReferenceRegion
org
root
originalCigar
AlignmentRecordField AlignmentRecord
originalQuality
AlignmentRecordField AlignmentRecord
originalStart
AlignmentRecordField AlignmentRecord
outputFormatClass
InstrumentedADAMBAMOutputFormat InstrumentedADAMBAMOutputFormatHeaderLess InstrumentedADAMCRAMOutputFormat InstrumentedADAMCRAMOutputFormatHeaderLess InstrumentedADAMSAMOutputFormat InstrumentedADAMSAMOutputFormatHeaderLess
outstream
AvroSerializer
overlaps
ReferenceRegion
overlapsBy
ReferenceRegion
overlapsReferencePosition
RichAlignmentRecord