GFF3InFormatter
feature
GFF3OutFormatter
feature
GTFInFormatter
feature
GTFOutFormatter
feature
GenomeBins
rdd
GenomicPositionPartitioner
rdd
GenomicRDD
rdd
GenomicRegionPartitioner
rdd
GenotypeField
projections
GenotypeRDD
variant
GetExtraValues
Timers
GetReferenceFromReads
Timers
GrowingTrees
Timers
gap
FeatureField
genbank
SequenceRecord
geneId
FeatureField TranscriptEffectField
geneName
TranscriptEffectField
genomicHgvs
TranscriptEffectField
genotype
DefaultHeaderLines
genotypeFilter
DefaultHeaderLines
genotypeLikelihoods
GenotypeField
genotypePriors
VariantCallingAnnotationsField
genotypeQuality
DefaultHeaderLines GenotypeField
genotypeToRichVariant
RichVariant
genotypes
VariantContext
get
GenomeBins
getEndBin
GenomeBins
getFiles
ADAMContext
getFsAndFiles
ADAMContext
getFsAndFilesWithFilter
ADAMContext
getIndex
RecordGroupDictionary
getMessage
IncorrectMDTagException
getPartition
GenomicPositionPartitioner GenomicRegionPartitioner ReferencePartitioner
getRecordWriter
ADAMBAMOutputFormat ADAMBAMOutputFormatHeaderLess ADAMCRAMOutputFormat ADAMCRAMOutputFormatHeaderLess ADAMSAMOutputFormat ADAMSAMOutputFormatHeaderLess ADAMHeaderlessVCFOutputFormat ADAMVCFOutputFormat
getReference
MdTag
getReferenceRegions
GenomicRDD NucleotideContigFragmentRDD CoverageRDD FeatureRDD FragmentRDD AlignmentRecordRDD GenotypeRDD VariantContextRDD VariantRDD
getStartBin
GenomeBins
gff3Parser
GFF3OutFormatter
gtSerializer
VariantContextSerializer
gtfParser
GTFOutFormatter