A
Base
ADAMAlignmentRecordContext
read
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read
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features
ADAMKryoRegistrator
serialization
ADAMMetrics
instrumentation
ADAMMetricsListener
instrumentation
ADAMNucleotideContigFragmentContext
contig
ADAMNucleotideContigFragmentRDDFunctions
contig
ADAMPileupContext
pileup
ADAMPileupRDDFunctions
pileup
ADAMPlugin
plugins
ADAMPredicate
predicates
ADAMRDDFunctions
rdd
ADAMRodRDDFunctions
pileup
ADAMSAMOutputFormat
read
ADAMSequenceDictionaryRDDAggregator
rdd
ADAMSparkMetrics
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rdd
ADAMVCFOutputFormat
variation
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variation
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ConcordanceTable
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aggregators
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converters
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index
AttrKey
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Attribute
models
AttributeUtils
util
AvroIndexedParquetRDD
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index
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parquet_reimpl
AvroSerializer
serialization
abbreviation
TypeVal
accepts
AndIndexPredicate IDRangeIndexPredicate IndexEntryPredicate OrIndexPredicate RangeIndexPredicate
accessKey
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adam
bdgenomics
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adamConvertToSAM
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adamDictionaryLoad
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adamDivideRodsBySamples
ADAMRodRDDFunctions
adamFilterRecordsWithTag
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adamFlagStat
ADAMAlignmentRecordRDDFunctions
adamFlatGenotypeReferenceFolder
ReferenceFoldingContext
adamGetCallsetSamples
VariantContextRDDFunctions
adamGetReadGroupDictionary
ADAMAlignmentRecordRDDFunctions
adamGetReferenceString
ADAMNucleotideContigFragmentRDDFunctions
adamGetSequenceDictionary
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adamKey
AttrKey
adamLoad
ADAMContext
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ADAMAlignmentRecordRDDFunctions
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adamPileupsToRods
ADAMPileupRDDFunctions
adamRealignIndels
ADAMAlignmentRecordRDDFunctions
adamRecords2Pileup
ADAMAlignmentRecordRDDFunctions
adamRecords2Rods
ADAMAlignmentRecordRDDFunctions
adamRewriteContigIds
ADAMNucleotideContigFragmentRDDFunctions
adamRodCoverage
ADAMRodRDDFunctions
adamSAMSave
ADAMAlignmentRecordRDDFunctions
adamSave
ADAMRDDFunctions
adamSequenceLoad
ADAMNucleotideContigFragmentContext
adamSingleReadBuckets
ADAMAlignmentRecordRDDFunctions
adamSortReadsByReferencePosition
ADAMAlignmentRecordRDDFunctions
adamSparkMetrics
ADAMMetrics
adamSplitRodsBySamples
ADAMRodRDDFunctions
adamTrimLowQualityReadGroups
ADAMAlignmentRecordRDDFunctions
adamTrimReads
ADAMAlignmentRecordRDDFunctions
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
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alleleFrequencyMLE
VariantCallingAnnotationsField
alleles
FlatGenotypeField GenotypeField
alternate
ReferenceAndAlternate
alternateAminoAcid
DatabaseVariantAnnotationField
alternateReadDepth
GenotypeField
alternating
NonoverlappingRegions
alts
VCFLine
ancestralAllele
DatabaseVariantAnnotationField
and
IndexEntryPredicate
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 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
asMap
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SequenceRecord
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attributes
AlignmentRecordField
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avro
parquet
avroSchema
ParquetLister IDRangeIndexGenerator RangeIndexGenerator
awsCredentials
CredentialsProperties