A
Base
ADAMBAMOutputFormat
util
ADAMContext
rdd
ADAMDatabaseVariantAnnotationField
projections
ADAMFeatureField
projections
ADAMFeaturesContext
features
ADAMFlatGenotypeField
projections
ADAMFlatGenotypeReferenceFolder
index
ADAMFlatGenotypeReferenceMapping
ReferenceMappingContext
ADAMGenotypeConditions
predicates
ADAMGenotypeField
variation
ADAMGenotypeRDDFunctions
variation
ADAMKryoRegistrator
serialization
ADAMMetrics
instrumentation
ADAMMetricsListener
instrumentation
ADAMNucleotideContigFragmentField
projections
ADAMNucleotideContigFragmentRDDFunctions
rdd
ADAMPileupRDDFunctions
rdd
ADAMPlugin
plugins
ADAMPredicate
predicates
ADAMRDDFunctions
rdd
ADAMRecordConditions
predicates
ADAMRecordConverter
converters
ADAMRecordField
projections
ADAMRecordRDDFunctions
rdd
ADAMRecordReferenceMapping
ReferenceMappingContext
ADAMRod
models
ADAMRodRDDFunctions
rdd
ADAMSAMOutputFormat
util
ADAMSequenceDictionaryRDDAggregator
rdd
ADAMSparkMetrics
ADAMMetrics
ADAMSpecificRecordSequenceDictionaryRDDAggregator
rdd
ADAMVCFOutputFormat
variation
ADAMVariantContext
models
ADAMVariantContextRDDFunctions
variation
ADAMVariantField
projections
ADAMVariationContext
variation
ALL
ConcordanceTable
ASCIITable
instrumentation
ASCIITableHeader
instrumentation
AbstractCovariate
recalibration
AccessControl
plugins
Aggregate
recalibration
Aggregated
aggregators
AggregatedCollection
aggregators
Aggregator
aggregators
Alignment
instrumentation Alignment
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
ADAMPileupRDDFunctions
adamAggregateRods
ADAMRodRDDFunctions
adamBEDFeatureLoad
ADAMFeaturesContext
adamBQSR
ADAMRecordRDDFunctions
adamBamLoad
ADAMContext
adamCharacterizeTagValues
ADAMRecordRDDFunctions
adamCharacterizeTags
ADAMRecordRDDFunctions
adamConvertToSAM
ADAMRecordRDDFunctions
adamCountKmers
ADAMRecordRDDFunctions
adamCountQmers
ADAMRecordRDDFunctions
adamDictionaryLoad
ADAMContext
adamDivideRodsBySamples
ADAMRodRDDFunctions
adamFilterRecordsWithTag
ADAMRecordRDDFunctions
adamFlagStat
ADAMRecordRDDFunctions
adamFlatGenotypeReferenceFolder
ReferenceFoldingContext
adamGetCallsetSamples
ADAMVariantContextRDDFunctions
adamGetReadGroupDictionary
ADAMRecordRDDFunctions
adamGetReferenceString
ADAMNucleotideContigFragmentRDDFunctions
adamGetSequenceDictionary
ADAMSequenceDictionaryRDDAggregator
adamKey
AttrKey
adamLoad
ADAMContext
adamMarkDuplicates
ADAMRecordRDDFunctions
adamMetrics
ADAMMetricsListener
adamNarrowPeakFeatureLoad
ADAMFeaturesContext
adamPileupsToRods
ADAMPileupRDDFunctions
adamRealignIndels
ADAMRecordRDDFunctions
adamRecords2Pileup
ADAMRecordRDDFunctions
adamRecords2Rods
ADAMRecordRDDFunctions
adamRewriteContigIds
ADAMNucleotideContigFragmentRDDFunctions
adamRodCoverage
ADAMRodRDDFunctions
adamSAMSave
ADAMRecordRDDFunctions
adamSave
ADAMRDDFunctions
adamSequenceLoad
ADAMContext
adamSingleReadBuckets
ADAMRecordRDDFunctions
adamSortReadsByReferencePosition
ADAMRecordRDDFunctions
adamSparkMetrics
ADAMMetrics
adamSplitRodsBySamples
ADAMRodRDDFunctions
adamTrimLowQualityReadGroups
ADAMRecordRDDFunctions
adamTrimReads
ADAMRecordRDDFunctions
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
ADAMFlatGenotypeField
alleleFrequencyMLE
VariantCallingAnnotationsField
alleles
ADAMFlatGenotypeField ADAMGenotypeField
alternate
ReferenceAndAlternate
alternateAminoAcid
ADAMDatabaseVariantAnnotationField
alternateReadDepth
ADAMGenotypeField
alternating
NonoverlappingRegions
alts
VCFLine
ancestralAllele
ADAMDatabaseVariantAnnotationField
and
IndexEntryPredicate
apply
DNAPrefixTrie IndelRealignmentTarget RealignmentTargetFinder TargetSet AttrKey Collection AggregatedCollection ADAMVariantContext IndelTable RecordGroup RecordGroupDictionary ReferencePosition ReferencePositionPair ReferencePositionWithOrientation ReferenceRegion ReferenceRegionWithOrientation SequenceDictionary SequenceRecord SingleReadBucket SnpTable ParquetOriginalType PrimitiveType Repetition TypePath AvroParquetFileMetadata ADAMPredicate Filter Projection CompressionCodecEnum DuplicateMetrics FlagStat GenomicRegionPartitioner GenotypesSummary GenotypesSummaryCounts MultiContigNonoverlappingRegions NonoverlappingRegions Aggregate BaseQualityRecalibration Covariate CovariateSpace Observation ObservationAccumulator RecalibrationTable Recalibrator ConcordanceTable DecadentRead RichADAMRecord RichCigar Histogram MdTag PileupTraversable QualityScore RegExp
asMap
BuildInformation
asString
BuildInformation
assembly
SequenceRecord
assertFilterValues
ParsedFilter
attrConverter
AttrKey
attrRegex
AttributeUtils
attributes
ADAMRecordField
averageReadDepthAtVariants
GenotypesSummaryCounts
avro
parquet
avroSchema
ParquetLister IDRangeIndexGenerator RangeIndexGenerator
awsCredentials
CredentialsProperties