GENBANK_TAG
SequenceRecord
GenomeBins
rdd
GenomicPositionPartitioner
rdd
GenomicRDD
rdd
GenomicRegionPartitioner
rdd
GenotypeField
projections
GenotypeRDD
variation
GetExtraValues
Timers
GetReferenceFromReads
Timers
gap
FeatureField
genbank
SequenceRecord
geneId
FeatureField
geneSymbol
DatabaseVariantAnnotationField
genotype
RichGenotype
genotypeLikelihoods
GenotypeField
genotypeQuality
GenotypeField
genotypeToRichGenotype
RichGenotype
genotypeToRichVariant
RichVariant
genotypes
VariantContext
gerpNr
DatabaseVariantAnnotationField
gerpRs
DatabaseVariantAnnotationField
get
GenomeBins
getEndBin
GenomeBins
getExtraValues
RecalibrationTable
getIndex
RecordGroupDictionary
getLength
RichCigar
getMessage
IncorrectMDTagException
getPartition
GenomicPositionPartitioner GenomicRegionPartitioner ReferencePartitioner
getQualityEntry
RecalibrationTable
getRecordWriter
ADAMBAMOutputFormat ADAMBAMOutputFormatHeaderLess ADAMCRAMOutputFormat ADAMCRAMOutputFormatHeaderLess ADAMSAMOutputFormat ADAMSAMOutputFormatHeaderLess ADAMHeaderlessVCFOutputFormat ADAMVCFOutputFormat
getReference
MdTag
getReferenceContext
RichAlignmentRecord
getReferenceRegions
GenomicRDD NucleotideContigFragmentRDD CoverageRDD FeatureRDD FragmentRDD AlignmentRecordRDD DatabaseVariantAnnotationRDD GenotypeRDD VariantContextRDD VariantRDD
getStartBin
GenomeBins
getType
RichGenotype
globalTable
RecalibrationTable
groupReadsByFragment
AlignmentRecordRDD