A
Base
ADAMBAMOutputFormat
read
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rdd
ADAMKryoRegistrator
serialization
ADAMParquetArgs
rdd
ADAMPlugin
plugins
ADAMPredicate
predicates
ADAMRDDFunctions
rdd
ADAMSAMOutputFormat
read
ADAMSaveAnyArgs
rdd
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rdd
ADAMSequenceDictionaryRDDAggregator
rdd
ADAMSpecificRecordSequenceDictionaryRDDAggregator
rdd
ADAMVCFOutputFormat
variation
ALL
ConcordanceTable
AbstractCovariate
recalibration
AccessControl
plugins
Aggregate
recalibration
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predicates
AlignmentRecordConverter
converters
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projections
AlignmentRecordRDDFunctions
read
AlignmentRecordReferenceMapping
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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
adamCountQmers
AlignmentRecordRDDFunctions
adamDictionaryLoad
ADAMContext
adamFilterRecordsWithTag
AlignmentRecordRDDFunctions
adamFlagStat
AlignmentRecordRDDFunctions
adamGetReadGroupDictionary
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adamGetReferenceString
NucleotideContigFragmentRDDFunctions
adamGetSequenceDictionary
ADAMSequenceDictionaryRDDAggregator
adamKey
AttrKey
adamLoad
ADAMContext
adamMarkDuplicates
AlignmentRecordRDDFunctions
adamParquetSave
ADAMRDDFunctions
adamPileupsToRods
PileupRDDFunctions
adamRePairReads
AlignmentRecordRDDFunctions
adamRealignIndels
AlignmentRecordRDDFunctions
adamRecords2Pileup
AlignmentRecordRDDFunctions
adamRecords2Rods
AlignmentRecordRDDFunctions
adamSAMSave
AlignmentRecordRDDFunctions
adamSAMString
AlignmentRecordRDDFunctions
adamSave
AlignmentRecordRDDFunctions
adamSaveAsFastq
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adamSaveAsPairedFastq
AlignmentRecordRDDFunctions
adamSingleReadBuckets
AlignmentRecordRDDFunctions
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AlignmentRecordRDDFunctions
adamTrimLowQualityReadGroups
AlignmentRecordRDDFunctions
adamTrimReads
AlignmentRecordRDDFunctions
adamVCFSave
VariantContextRDDFunctions
add
ConcordanceTable MapTools
addHeader
ADAMBAMOutputFormat ADAMSAMOutputFormat
aggregate
ObservationTable
aggregateStatistics
GenotypesSummary
algorithms
adam
alignmentQuality
DecadentRead
allReads
ReadBucket SingleReadBucket
allSNVs
GenotypesSummaryFormatting
alleleCountMLE
VariantCallingAnnotationsField
alleleFrequencyMLE
VariantCallingAnnotationsField
alleles
GenotypeField
alternate
ReferenceAndAlternate
alternateAminoAcid
DatabaseVariantAnnotationField
alternateReadDepth
GenotypeField
alternating
NonoverlappingRegions
ancestralAllele
DatabaseVariantAnnotationField
and
RecordCondition
apply
DNAPrefixTrie AttrKey IndelTable ProgramRecord RecordGroup RecordGroupDictionary ReferencePosition ReferencePositionPair ReferencePositionWithOrientation ReferenceRegion ReferenceRegionWithOrientation SAMFileHeaderWritable SequenceDictionary SequenceRecord SingleReadBucket SnpTable VariantContext ADAMPredicate AlignmentRecordConditions FieldCondition PredicateUtils RecordCondition Filter Projection GenomicPositionPartitioner GenomicRegionPartitioner MultiContigNonoverlappingRegions NonoverlappingRegions LengthNormalization ZScoreNormalization DuplicateMetrics FlagStat IndelRealignmentTarget RealignmentTargetFinder TargetSet Aggregate BaseQualityRecalibration Covariate CovariateSpace Observation ObservationAccumulator RecalibrationTable Recalibrator ConcordanceTable GenotypesSummary GenotypesSummaryCounts DecadentRead RichAlignmentRecord RichCigar MdTag PileupTraversable QualityScore RegExp TwoBitRecord
applyPredicate
ADAMContext
asGenes
GeneFeatureRDDFunctions
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