A
Base
ADAMBAMOutputFormat
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projections
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predicates
ADAMGenotypeField
variation
ADAMGenotypeRDDFunctions
variation
ADAMKryoRegistrator
serialization
ADAMNucleotideContigFragmentField
projections
ADAMNucleotideContigFragmentRDDFunctions
rdd
ADAMPileupRDDFunctions
rdd
ADAMPlugin
plugins
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predicates
ADAMRDDFunctions
rdd
ADAMRecordConditions
predicates
ADAMRecordConverter
converters
ADAMRecordField
projections
ADAMRecordRDDFunctions
rdd
ADAMRecordReferenceMapping
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ADAMRod
models
ADAMRodRDDFunctions
rdd
ADAMSAMOutputFormat
util
ADAMSequenceDictionaryRDDAggregator
rdd
ADAMSpecificRecordSequenceDictionaryRDDAggregator
rdd
ADAMVCFOutputFormat
variation
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models
ADAMVariantContextRDDFunctions
variation
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adamCharacterizeTags
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adamDictionaryLoad
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adamDivideRodsBySamples
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adamFilterRecordsWithTag
ADAMRecordRDDFunctions
adamFlagStat
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adamGetCallsetSamples
ADAMVariantContextRDDFunctions
adamGetReadGroupDictionary
ADAMRecordRDDFunctions
adamGetReferenceString
ADAMNucleotideContigFragmentRDDFunctions
adamGetSequenceDictionary
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adamKey
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adamMarkDuplicates
ADAMRecordRDDFunctions
adamPileupsToRods
ADAMPileupRDDFunctions
adamRealignIndels
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adamRecordToReferenceMapped
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adamRecords2Pileup
ADAMRecordRDDFunctions
adamRecords2Rods
ADAMRecordRDDFunctions
adamRewriteContigIds
ADAMNucleotideContigFragmentRDDFunctions
adamRodCoverage
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adamSAMSave
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adamSave
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adamSequenceLoad
ADAMContext
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ADAMRecordRDDFunctions
adamSortReadsByReferencePosition
ADAMRecordRDDFunctions
adamSplitRodsBySamples
ADAMRodRDDFunctions
adamTrimLowQualityReadGroups
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alignmentQuality
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allReads
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alleleArray
VCFLine
alleleCountMLE
VariantCallingAnnotationsField
alleleDepths
ADAMFlatGenotypeField
alleleFrequencyMLE
VariantCallingAnnotationsField
alleles
ADAMFlatGenotypeField ADAMGenotypeField
alternate
ReferenceAndAlternate
alternateAminoAcid
ADAMDatabaseVariantAnnotationField
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alternating
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alts
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ADAMDatabaseVariantAnnotationField
apply
IndelRealignmentTarget RealignmentTargetFinder AttrKey Collection AggregatedCollection ADAMVariantContext RecordGroupDictionary ReferencePosition ReferencePositionPair ReferencePositionWithOrientation ReferenceRegion SequenceDictionary SequenceRecord SingleReadBucket SnpTable ADAMPredicate Filter Projection 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
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asString
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SequenceRecord
assertFilterValues
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attrConverter
AttrKey
attrRegex
AttributeUtils
attributes
ADAMRecordField
averageReadDepthAtVariants
GenotypesSummaryCounts
awsCredentials
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