GENBANK_TAG
SequenceRecord
GTFFeature
models
GTFParser
features
Gene
models
GeneFeatureRDDFunctions
features
GenomeBins
rdd
GenomicPositionPartitioner
rdd
GenomicRegionPartitioner
rdd
GenotypeField
projections
GenotypeRDDFunctions
variation
GetExtraValues
Timers
GetReferenceFromReads
Timers
genbank
SequenceRecord
geneId
Transcript
geneSymbol
DatabaseVariantAnnotationField
generateAlternateConsensus
Consensus
genotype
RichGenotype
genotypeLikelihoods
GenotypeField
genotypeQuality
GenotypeField
genotypeToRichGenotype
RichGenotype
genotypes
VariantContext
gerpNr
DatabaseVariantAnnotationField
gerpRs
DatabaseVariantAnnotationField
get
GenomeBins
getAllWindows
Coverage
getAttribute
GTFFeature
getBlockCount
BEDFeature
getBlockSizes
BEDFeature
getBlockStarts
BEDFeature
getCallsetSamples
VariantContextRDDFunctions
getChrom
BEDFeature NarrowPeakFeature
getChromEnd
BEDFeature NarrowPeakFeature
getChromStart
BEDFeature NarrowPeakFeature
getEnd
GTFFeature
getEndBin
GenomeBins
getExtraValues
RecalibrationTable
getFeature
GTFFeature
getFrame
GTFFeature
getHeader
ADAMVCFOutputFormat
getIndelsInRegion
IndelTable
getIndex
RecordGroupDictionary
getItemRGB
BEDFeature
getLength
RichCigar
getName
BEDFeature NarrowPeakFeature
getPValue
NarrowPeakFeature
getPartition
GenomicPositionPartitioner GenomicRegionPartitioner ReferencePartitioner
getPeak
NarrowPeakFeature
getQValue
NarrowPeakFeature
getQualityEntry
RecalibrationTable
getReference
MdTag
getReferenceContext
RichAlignmentRecord
getScore
BEDFeature GTFFeature NarrowPeakFeature
getSeqname
GTFFeature
getSequenceRecordsFromElement
ADAMSequenceDictionaryRDDAggregator ADAMSpecificRecordSequenceDictionaryRDDAggregator NucleotideContigFragmentRDDFunctions AlignmentRecordRDDFunctions VariantContextRDDFunctions
getSignalValue
NarrowPeakFeature
getSource
GTFFeature
getStart
GTFFeature
getStartBin
GenomeBins
getStrand
BEDFeature GTFFeature NarrowPeakFeature
getThickEnd
BEDFeature
getThickStart
BEDFeature
getType
RichGenotype
globalTable
RecalibrationTable