A
Base
ADAMBAMOutputFormat
read
ADAMContext
rdd
ADAMKryoRegistrator
serialization
ADAMMetrics
instrumentation
ADAMMetricsListener
instrumentation
ADAMParquetArgs
rdd
ADAMPlugin
plugins
ADAMPredicate
predicates
ADAMRDDFunctions
rdd
ADAMSAMOutputFormat
read
ADAMSaveAnyArgs
rdd
ADAMSaveArgs
rdd
ADAMSequenceDictionaryRDDAggregator
rdd
ADAMSparkMetrics
ADAMMetrics
ADAMSpecificRecordSequenceDictionaryRDDAggregator
rdd
ADAMVCFOutputFormat
variation
ALL
ConcordanceTable
ASCIITable
instrumentation
ASCIITableHeader
instrumentation
AbstractCovariate
recalibration
AccessControl
plugins
Aggregate
recalibration
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aggregators
AggregatedCollection
aggregators
Aggregator
aggregators
Alignment
instrumentation Alignment
AlignmentRecordConditions
predicates
AlignmentRecordContext
read
AlignmentRecordConverter
converters
AlignmentRecordField
projections
AlignmentRecordRDDFunctions
read
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
adamAlignedRecordSave
AlignmentRecordRDDFunctions
adamBEDFeatureLoad
FeaturesContext
adamBQSR
AlignmentRecordRDDFunctions
adamCharacterizeTagValues
AlignmentRecordRDDFunctions
adamCharacterizeTags
AlignmentRecordRDDFunctions
adamContextToADAMContext
AlignmentRecordContext
adamConvertToSAM
AlignmentRecordRDDFunctions
adamCountKmers
AlignmentRecordRDDFunctions
adamCountQmers
AlignmentRecordRDDFunctions
adamDictionaryLoad
ADAMContext
adamFastqLoad
AlignmentRecordContext
adamFilterRecordsWithTag
AlignmentRecordRDDFunctions
adamFlagStat
AlignmentRecordRDDFunctions
adamFlatGenotypeReferenceFolder
ReferenceFoldingContext
adamGTFFeatureLoad
FeaturesContext
adamGetReadGroupDictionary
AlignmentRecordRDDFunctions
adamGetReferenceString
NucleotideContigFragmentRDDFunctions
adamGetSequenceDictionary
ADAMSequenceDictionaryRDDAggregator
adamKey
AttrKey
adamLoad
ADAMContext
adamMarkDuplicates
AlignmentRecordRDDFunctions
adamMetrics
ADAMMetricsListener
adamNarrowPeakFeatureLoad
FeaturesContext
adamParquetSave
ADAMRDDFunctions
adamPileupsToRods
PileupRDDFunctions
adamRealignIndels
AlignmentRecordRDDFunctions
adamRecords2Pileup
AlignmentRecordRDDFunctions
adamRecords2Rods
AlignmentRecordRDDFunctions
adamSAMSave
AlignmentRecordRDDFunctions
adamSAMString
AlignmentRecordRDDFunctions
adamSave
AlignmentRecordRDDFunctions
adamSaveAsFastq
AlignmentRecordRDDFunctions
adamSaveAsPairedFastq
AlignmentRecordRDDFunctions
adamSequenceLoad
NucleotideContigFragmentContext
adamSingleReadBuckets
AlignmentRecordRDDFunctions
adamSortReadsByReferencePosition
AlignmentRecordRDDFunctions
adamSparkMetrics
ADAMMetrics
adamTrimLowQualityReadGroups
AlignmentRecordRDDFunctions
adamTrimReads
AlignmentRecordRDDFunctions
adamVCFAnnotationLoad
VariationContext
adamVCFLoad
VariationContext
adamVCFSave
VariationContext
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 RecordCondition
apply
DNAPrefixTrie AttrKey Collection AggregatedCollection IndelTable ProgramRecord RecordGroup RecordGroupDictionary ReferencePosition ReferencePositionPair ReferencePositionWithOrientation ReferenceRegion ReferenceRegionWithOrientation SAMFileHeaderWritable SequenceDictionary SequenceRecord SingleReadBucket SnpTable VariantContext ParquetOriginalType PrimitiveType Repetition TypePath AvroParquetFileMetadata ADAMPredicate AlignmentRecordConditions FieldCondition PredicateUtils RecordCondition Filter Projection CompressionCodecEnum GenomicRegionPartitioner MultiContigNonoverlappingRegions NonoverlappingRegions LengthNormalization ZScoreNormalization DuplicateMetrics FlagStat IndelRealignmentTarget RealignmentTargetFinder TargetSet Aggregate BaseQualityRecalibration Covariate CovariateSpace Observation ObservationAccumulator RecalibrationTable Recalibrator ConcordanceTable GenotypesSummary GenotypesSummaryCounts DecadentRead RichAlignmentRecord RichCigar Histogram MdTag PileupTraversable QualityScore RegExp
applyPredicate
ADAMContext
asGenes
GeneFeatureRDD
asMap
BuildInformation
asString
BuildInformation
assembly
SequenceRecord
assertFilterValues
ParsedFilter
attrConverter
AttrKey
attrRegex
AttributeUtils
attributeDouble
BaseFeature
attributeInt
BaseFeature
attributeLong
BaseFeature
attributeString
BaseFeature
attributes
AlignmentRecordField FeatureField
attrs
BaseFeature
averageReadDepthAtVariants
GenotypesSummaryCounts
avro
parquet
avroSchema
ParquetLister IDRangeIndexGenerator RangeIndexGenerator
awsCredentials
CredentialsProperties