ADAMBAMOutputFormat
read
ADAMContext
rdd
ADAMKryoRegistrator
serialization
ADAMPlugin
plugins
ADAMRDDFunctions
rdd
ADAMSAMOutputFormat
read
ADAMSaveAnyArgs
rdd
ADAMSequenceDictionaryRDDAggregator
rdd
ADAMSpecificRecordSequenceDictionaryRDDAggregator
rdd
ADAMVCFOutputFormat
variation
AbstractCovariate
recalibration
AccessControl
plugins
Aggregate
recalibration
AlignmentRecordConverter
converters
AlignmentRecordField
projections
AlignmentRecordRDDFunctions
read
Alphabet
models
AttrKey
converters
Attribute
models
AttributeUtils
util
AvroSerializer
serialization
abbreviation
TypeVal
accum
ObservationAccumulator
adam
bdgenomics
adamAlignedRecordSave
AlignmentRecordRDDFunctions
adamBQSR
AlignmentRecordRDDFunctions
adamCharacterizeTagValues
AlignmentRecordRDDFunctions
adamCharacterizeTags
AlignmentRecordRDDFunctions
adamConvertToSAM
AlignmentRecordRDDFunctions
adamCountKmers
AlignmentRecordRDDFunctions
adamDictionaryLoad
ADAMContext
adamFilterRecordsWithTag
AlignmentRecordRDDFunctions
adamFlagStat
AlignmentRecordRDDFunctions
adamGetReadGroupDictionary
AlignmentRecordRDDFunctions
adamGetReferenceString
NucleotideContigFragmentRDDFunctions
adamGetSequenceDictionary
ADAMSequenceDictionaryRDDAggregator
adamKey
AttrKey
adamMarkDuplicates
AlignmentRecordRDDFunctions
adamParquetSave
ADAMRDDFunctions
adamRePairReads
AlignmentRecordRDDFunctions
adamRealignIndels
AlignmentRecordRDDFunctions
adamSAMSave
AlignmentRecordRDDFunctions
adamSAMString
AlignmentRecordRDDFunctions
adamSave
AlignmentRecordRDDFunctions
adamSaveAsFastq
AlignmentRecordRDDFunctions
adamSaveAsPairedFastq
AlignmentRecordRDDFunctions
adamSingleReadBuckets
AlignmentRecordRDDFunctions
adamSortReadsByReferencePosition
AlignmentRecordRDDFunctions
add
MapTools
addHeader
ADAMBAMOutputFormat ADAMSAMOutputFormat
aggregateObservations
RecalibrationTable
algorithms
adam
alignmentQuality
DecadentRead
allReads
ReadBucket SingleReadBucket
alleleCountMLE
VariantCallingAnnotationsField
alleleFrequencyMLE
VariantCallingAnnotationsField
alleles
GenotypeField
alternateAminoAcid
DatabaseVariantAnnotationField
alternateReadDepth
GenotypeField
ancestralAllele
DatabaseVariantAnnotationField
apply
AttrKey Alphabet IndelTable ProgramRecord RecordGroup RecordGroupDictionary ReferencePosition ReferencePositionPair ReferenceRegion SAMFileHeaderWritable SequenceDictionary SequenceRecord SingleReadBucket SnpTable VariantContext Filter Projection GenomicPositionPartitioner GenomicRegionPartitioner DuplicateMetrics FlagStat IndelRealignmentTarget RealignmentTargetFinder TargetSet Aggregate BaseQualityRecalibration Covariate CovariateSpace Observation ObservationAccumulator RecalibrationTable Recalibrator DecadentRead RichAlignmentRecord RichCigar MdTag QualityScore RegExp TwoBitRecord
asGenes
GeneFeatureRDDFunctions
asMap
BuildInformation
asString
BuildInformation
assembly
SequenceRecord
attrConverter
AttrKey
attrRegex
AttributeUtils
attributeDouble
BaseFeature
attributeInt
BaseFeature
attributeLong
BaseFeature
attributeString
BaseFeature
attributes
AlignmentRecordField FeatureField
attrs
BaseFeature