A
Base
ADAMBAMOutputFormat
util
ADAMContext
rdd
ADAMFeaturesContext
features
ADAMKryoRegistrator
serialization
ADAMMetrics
instrumentation
ADAMMetricsListener
instrumentation
ADAMPlugin
plugins
ADAMPredicate
predicates
ADAMRDDFunctions
rdd
ADAMSAMOutputFormat
util
ADAMSequenceDictionaryRDDAggregator
rdd
ADAMSparkMetrics
ADAMMetrics
ADAMSpecificRecordSequenceDictionaryRDDAggregator
rdd
ADAMVCFOutputFormat
variation
ADAMVariationContext
variation
ALL
ConcordanceTable
ASCIITable
instrumentation
ASCIITableHeader
instrumentation
AbstractCovariate
recalibration
AccessControl
plugins
Aggregate
recalibration
Aggregated
aggregators
AggregatedCollection
aggregators
Aggregator
aggregators
Alignment
instrumentation Alignment
AlignmentRecordConditions
predicates
AlignmentRecordConverter
converters
AlignmentRecordField
projections
AlignmentRecordRDDFunctions
rdd
AlignmentRecordReferenceMapping
ReferenceMappingContext
AndIndexPredicate
index
AttrKey
converters
Attribute
models
AttributeUtils
util
AvroIndexedParquetRDD
parquet_reimpl
AvroParquetFileMetadata
index
AvroParquetRDD
parquet_reimpl
AvroSerializer
serialization
abbreviation
TypeVal
accepts
AndIndexPredicate IDRangeIndexPredicate IndexEntryPredicate OrIndexPredicate RangeIndexPredicate
accessKey
CredentialsProperties
accum
ObservationAccumulator
actualSchema
ParquetPartition ParquetFileMetadata
adam
bdgenomics
adamAggregatePileups
PileupRDDFunctions
adamAggregateRods
RodRDDFunctions
adamBEDFeatureLoad
ADAMFeaturesContext
adamBQSR
AlignmentRecordRDDFunctions
adamBamLoad
ADAMContext
adamCharacterizeTagValues
AlignmentRecordRDDFunctions
adamCharacterizeTags
AlignmentRecordRDDFunctions
adamConvertToSAM
AlignmentRecordRDDFunctions
adamCountKmers
AlignmentRecordRDDFunctions
adamCountQmers
AlignmentRecordRDDFunctions
adamDictionaryLoad
ADAMContext
adamDivideRodsBySamples
RodRDDFunctions
adamFilterRecordsWithTag
AlignmentRecordRDDFunctions
adamFlagStat
AlignmentRecordRDDFunctions
adamFlatGenotypeReferenceFolder
ReferenceFoldingContext
adamGetCallsetSamples
VariantContextRDDFunctions
adamGetReadGroupDictionary
AlignmentRecordRDDFunctions
adamGetReferenceString
NucleotideContigFragmentRDDFunctions
adamGetSequenceDictionary
ADAMSequenceDictionaryRDDAggregator
adamKey
AttrKey
adamLoad
ADAMContext
adamMarkDuplicates
AlignmentRecordRDDFunctions
adamMetrics
ADAMMetricsListener
adamNarrowPeakFeatureLoad
ADAMFeaturesContext
adamPileupsToRods
PileupRDDFunctions
adamRealignIndels
AlignmentRecordRDDFunctions
adamRecords2Pileup
AlignmentRecordRDDFunctions
adamRecords2Rods
AlignmentRecordRDDFunctions
adamRewriteContigIds
NucleotideContigFragmentRDDFunctions
adamRodCoverage
RodRDDFunctions
adamSAMSave
AlignmentRecordRDDFunctions
adamSave
ADAMRDDFunctions
adamSequenceLoad
ADAMContext
adamSingleReadBuckets
AlignmentRecordRDDFunctions
adamSortReadsByReferencePosition
AlignmentRecordRDDFunctions
adamSparkMetrics
ADAMMetrics
adamSplitRodsBySamples
RodRDDFunctions
adamTrimLowQualityReadGroups
AlignmentRecordRDDFunctions
adamTrimReads
AlignmentRecordRDDFunctions
adamVCFAnnotationLoad
ADAMVariationContext
adamVCFLoad
ADAMVariationContext
adamVCFSave
ADAMVariationContext
add
ConcordanceTable MapTools
addHeader
ADAMBAMOutputFormat ADAMSAMOutputFormat
addParquetFile
IDRangeIndexGenerator RangeIndexGenerator
addTag
ServoTimer Taggable
aggregate
ObservationTable
aggregateStatistics
GenotypesSummary
aggregators
metrics
algorithms
adam
alignment
ASCIITableHeader TableHeader
alignmentQuality
DecadentRead
allReads
ReadBucket SingleReadBucket
allSNVs
GenotypesSummaryFormatting
alleleArray
VCFLine
alleleCountMLE
VariantCallingAnnotationsField
alleleDepths
FlatGenotypeField
alleleFrequencyMLE
VariantCallingAnnotationsField
alleles
FlatGenotypeField GenotypeField
alternate
ReferenceAndAlternate
alternateAminoAcid
DatabaseVariantAnnotationField
alternateReadDepth
GenotypeField
alternating
NonoverlappingRegions
alts
VCFLine
ancestralAllele
DatabaseVariantAnnotationField
and
IndexEntryPredicate
apply
DNAPrefixTrie IndelRealignmentTarget RealignmentTargetFinder TargetSet AttrKey Collection AggregatedCollection IndelTable RecordGroup RecordGroupDictionary ReferencePosition ReferencePositionPair ReferencePositionWithOrientation ReferenceRegion ReferenceRegionWithOrientation SequenceDictionary SequenceRecord SingleReadBucket SnpTable VariantContext ParquetOriginalType PrimitiveType Repetition TypePath AvroParquetFileMetadata ADAMPredicate Filter Projection CompressionCodecEnum DuplicateMetrics FlagStat GenomicRegionPartitioner GenotypesSummary GenotypesSummaryCounts MultiContigNonoverlappingRegions NonoverlappingRegions LengthNormalization ZScoreNormalization Aggregate BaseQualityRecalibration Covariate CovariateSpace Observation ObservationAccumulator RecalibrationTable Recalibrator ConcordanceTable DecadentRead RichAlignmentRecord RichCigar Histogram MdTag PileupTraversable QualityScore RegExp
asMap
BuildInformation
asString
BuildInformation
assembly
SequenceRecord
assertFilterValues
ParsedFilter
attrConverter
AttrKey
attrRegex
AttributeUtils
attributes
AlignmentRecordField
averageReadDepthAtVariants
GenotypesSummaryCounts
avro
parquet
avroSchema
ParquetLister IDRangeIndexGenerator RangeIndexGenerator
awsCredentials
CredentialsProperties