GFF3InFormatter
feature
GFF3OutFormatter
feature
GTFInFormatter
feature
GTFOutFormatter
feature
GenericConverter
rdd
GenericGenomicDataset
rdd
GenomeBins
rdd
GenomeFileReader
util
GenomicBroadcast
rdd
GenomicDataset
rdd
GenomicDatasetConversion
rdd
GenomicDatasetWithLineage
rdd
GenomicPositionPartitioner
rdd
GenomicRegionPartitioner
rdd
Genotype
sql
GenotypeDataset
variant
GenotypeField
projections
GetExtraValues
Timers
GetReferenceFromFile
Timers
GetReferenceFromReads
Timers
GrowingTrees
Timers
gap
FeatureField Feature
genbank
SequenceRecord
geneId
FeatureField TranscriptEffectField Feature TranscriptEffect
geneName
TranscriptEffectField TranscriptEffect
genericToAlignmentsConversionFn
ADAMContext
genericToCoverageConversionFn
ADAMContext
genericToFeatureConversionFn
ADAMContext
genericToFragmentsConversionFn
ADAMContext
genericToGenotypesConversionFn
ADAMContext
genericToReadsConversionFn
ADAMContext
genericToSequencesConversionFn
ADAMContext
genericToSlicesConversionFn
ADAMContext
genericToVariantContextsConversionFn
ADAMContext
genericToVariantsConversionFn
ADAMContext
genomicHgvs
TranscriptEffectField TranscriptEffect
genotype
DefaultHeaderLines
genotypeFilter
DefaultHeaderLines
genotypeHeaders
ADAMShell
genotypeLikelihoods
GenotypeField Genotype
genotypePosteriors
VariantCallingAnnotationsField VariantCallingAnnotations
genotypePriors
VariantCallingAnnotationsField VariantCallingAnnotations
genotypeQuality
DefaultHeaderLines GenotypeField Genotype
genotypeToRichVariant
RichVariant
genotypes
VariantContext VariantContext
genotypesToAlignmentsConversionFn
ADAMContext
genotypesToAlignmentsDatasetConversionFn
ADAMContext
genotypesToCoverageConversionFn
ADAMContext
genotypesToCoverageDatasetConversionFn
ADAMContext
genotypesToFeaturesConversionFn
ADAMContext
genotypesToFeaturesDatasetConversionFn
ADAMContext
genotypesToFragmentsConversionFn
ADAMContext
genotypesToFragmentsDatasetConversionFn
ADAMContext
genotypesToGenotypesConversionFn
ADAMContext
genotypesToReadsConversionFn
ADAMContext
genotypesToReadsDatasetConversionFn
ADAMContext
genotypesToSequencesConversionFn
ADAMContext
genotypesToSequencesDatasetConversionFn
ADAMContext
genotypesToSlicesConversionFn
ADAMContext
genotypesToSlicesDatasetConversionFn
ADAMContext
genotypesToVariantContextConversionFn
ADAMContext
genotypesToVariantsConversionFn
ADAMContext
genotypesToVariantsDatasetConversionFn
ADAMContext
get
GenomeBins
getCurrentKey
FastqRecordReader
getCurrentValue
FastqRecordReader
getEndBin
GenomeBins
getFiles
ADAMContext
getFsAndFiles
ADAMContext
getFsAndFilesWithFilter
ADAMContext
getIndex
ReadGroupDictionary
getMessage
IncorrectMDTagException
getPartition
GenomicPositionPartitioner GenomicRegionPartitioner ReferencePartitioner
getProgress
FastqRecordReader
getRecordWriter
ADAMBAMOutputFormat ADAMBAMOutputFormatHeaderLess ADAMCRAMOutputFormat ADAMCRAMOutputFormatHeaderLess ADAMSAMOutputFormat ADAMSAMOutputFormatHeaderLess ADAMVCFOutputFormat
getReference
MdTag
getReferenceRegions
GenericGenomicDataset GenomicDataset CoverageDataset FeatureDataset FragmentDataset AlignmentDataset ReadDataset SequenceDataset SliceDataset GenotypeDataset VariantContextDataset VariantDataset
getStartBin
GenomeBins
gff3Parser
GFF3OutFormatter
gtSerializer
VariantContextSerializer
gtfParser
GTFOutFormatter