SAMInFormatter
read
SAMSave
Timers
SampleField
projections
SaveAsADAM
Timers
SaveAsVcf
Timers
SchemaVal
FieldEnumeration
SchemaValue
FieldEnumeration
ScoreAndMarkReads
Timers
Sequence
sql
SequenceDataset
sequence
SequenceDictionary
models
SequenceDictionaryReader
util
SequenceField
projections
SequenceRecord
models
ShuffleJoinAndGroupByLeft
Timers
ShuffleRegionJoin
rdd
SingleFastqInputFormat
io
SingleReadBucketSerializer
read
Slice
sql
SliceDataset
sequence
SliceField
projections
SmithWaterman
smithwaterman
SmithWatermanConstantGapScoring
smithwaterman
SnpTable
models
SortAlignments
Timers
SortAlignmentsByIndex
Timers
SortTargets
Timers
SortedIntervalPartitionJoinWithVictims
rdd
SortingRightSide
Timers
String
TagType
SweepReadOverReferenceForQuality
Timers
SweepReadsOverConsensus
Timers
Symbol
models
sameReferenceName
ReferenceRegion
sameStrand
ReferenceRegion
sampleDescription
GenotypeField Genotype
sampleId
ReadGroup FeatureField GenotypeField ReadGroupField Feature Genotype
samples
MultisampleGenomicDataset DatasetBoundCoverageDataset DatasetBoundFeatureDataset ParquetUnboundCoverageDataset ParquetUnboundFeatureDataset RDDBoundCoverageDataset RDDBoundFeatureDataset DatasetBoundGenotypeDataset DatasetBoundVariantContextDataset ParquetUnboundGenotypeDataset RDDBoundGenotypeDataset RDDBoundVariantContextDataset VCFInFormatter
samtoolsCigar
RichAlignment
save
CoverageDataset FeatureDataset FragmentDataset AlignmentDataset ReadDataset SequenceDataset SliceDataset
saveAsBed
FeatureDataset
saveAsFasta
SequenceDataset SliceDataset
saveAsFastq
AlignmentDataset ReadDataset
saveAsGff3
FeatureDataset
saveAsGtf
FeatureDataset
saveAsIntervalList
FeatureDataset
saveAsNarrowPeak
FeatureDataset
saveAsPairedFastq
AlignmentDataset
saveAsParquet
AvroGenomicDataset GenericGenomicDataset GenomicDataset CoverageDataset DatasetBoundFeatureDataset DatasetBoundFragmentDataset DatasetBoundAlignmentDataset DatasetBoundReadDataset DatasetBoundSequenceDataset DatasetBoundSliceDataset DatasetBoundGenotypeDataset DatasetBoundVariantDataset VariantContextDataset
saveAsPartitionedParquet
GenomicDataset
saveAsSam
AlignmentDataset
saveAsSamString
AlignmentDataset
saveAsUcscBed
FeatureDataset
saveAsVcf
VariantContextDataset
saveAvro
GenomicDataset
saveMetadata
AvroGenomicDataset AvroReadGroupGenomicDataset GenomicDataset MultisampleAvroGenomicDataset FeatureDataset GenotypeDataset VariantContextDataset VariantDataset
savePartitionMap
AvroGenomicDataset
saveProcessingSteps
AvroReadGroupGenomicDataset
saveRddAsParquet
AvroGenomicDataset
saveReadGroups
AvroReadGroupGenomicDataset
saveSamples
MultisampleGenomicDataset
saveSequences
GenomicDataset
saveVcfHeaders
GenotypeDataset VariantContextDataset VariantDataset
sc
ADAMContext IndexedFastaFile
schema
SchemaVal FieldValue
score
FeatureField QualityScoreBin Feature
scoreFn
SmithWatermanConstantGapScoring
sd
ReferencePartitioner
secondaryAlignment
AlignmentField Alignment
seqLengths
GenomeBins GenomicPositionPartitioner GenomicRegionPartitioner
sequence
AlignmentField ReadField SequenceField SliceField rdd Alignment Read Sequence Slice
sequenceHeaders
ADAMShell
sequences
DatasetBoundGenericGenomicDataset GenomicDataset RDDBoundGenericGenomicDataset DatasetBoundCoverageDataset DatasetBoundFeatureDataset ParquetUnboundCoverageDataset ParquetUnboundFeatureDataset RDDBoundCoverageDataset RDDBoundFeatureDataset DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset DatasetBoundAlignmentDataset DatasetBoundReadDataset ParquetUnboundAlignmentDataset ParquetUnboundReadDataset RDDBoundAlignmentDataset RDDBoundReadDataset DatasetBoundSequenceDataset DatasetBoundSliceDataset ParquetUnboundSequenceDataset ParquetUnboundSliceDataset RDDBoundSequenceDataset RDDBoundSliceDataset DatasetBoundGenotypeDataset DatasetBoundVariantContextDataset DatasetBoundVariantDataset ParquetUnboundGenotypeDataset ParquetUnboundVariantDataset RDDBoundGenotypeDataset RDDBoundVariantContextDataset RDDBoundVariantDataset VCFInFormatter IndexedFastaFile ReferenceContigMap ReferenceFile TwoBitFile
sequencesToAlignmentsConversionFn
ADAMContext
sequencesToAlignmentsDatasetConversionFn
ADAMContext
sequencesToCoverageConversionFn
ADAMContext
sequencesToCoverageDatasetConversionFn
ADAMContext
sequencesToFeaturesConversionFn
ADAMContext
sequencesToFeaturesDatasetConversionFn
ADAMContext
sequencesToFragmentsConversionFn
ADAMContext
sequencesToFragmentsDatasetConversionFn
ADAMContext
sequencesToGenotypesConversionFn
ADAMContext
sequencesToGenotypesDatasetConversionFn
ADAMContext
sequencesToReadsConversionFn
ADAMContext
sequencesToReadsDatasetConversionFn
ADAMContext
sequencesToSequencesConversionFn
ADAMContext
sequencesToSlicesConversionFn
ADAMContext
sequencesToSlicesDatasetConversionFn
ADAMContext
sequencesToVariantContextsConversionFn
ADAMContext
sequencesToVariantsConversionFn
ADAMContext
sequencesToVariantsDatasetConversionFn
ADAMContext
sequencingCenter
ReadGroup ReadGroupField
serialization
adam
setNestAnnotationInGenotypesProperty
VariantContextConverter
shuffleRegionJoin
GenomicDataset
shuffleRegionJoinAndGroupByLeft
GenomicDataset
size
Alphabet ReadGroupDictionary SequenceDictionary InputStreamWithDecoder
slice
SequenceDataset
sliceHeaders
ADAMShell
slices
SliceField Slice
slicesToAlignmentsConversionFn
ADAMContext
slicesToAlignmentsDatasetConversionFn
ADAMContext
slicesToCoverageConversionFn
ADAMContext
slicesToCoverageDatasetConversionFn
ADAMContext
slicesToFeaturesConversionFn
ADAMContext
slicesToFeaturesDatasetConversionFn
ADAMContext
slicesToFragmentsConversionFn
ADAMContext
slicesToFragmentsDatasetConversionFn
ADAMContext
slicesToGenotypesConversionFn
ADAMContext
slicesToGenotypesDatasetConversionFn
ADAMContext
slicesToReadsConversionFn
ADAMContext
slicesToReadsDatasetConversionFn
ADAMContext
slicesToSequencesConversionFn
ADAMContext
slicesToSequencesDatasetConversionFn
ADAMContext
slicesToSlicesConversionFn
ADAMContext
slicesToVariantContextsConversionFn
ADAMContext
slicesToVariantsConversionFn
ADAMContext
slicesToVariantsDatasetConversionFn
ADAMContext
smithwaterman
algorithms
somatic
DefaultHeaderLines VariantAnnotationField VariantAnnotation
sort
GenomicDataset
sortByReadName
AlignmentDataset
sortByReference
FeatureDataset
sortByReferencePosition
AlignmentDataset
sortByReferencePositionAndIndex
AlignmentDataset
sortFastqOutput
ADAMSaveAnyArgs
sortLexicographically
GenomicDataset
sorted
SequenceDictionary
source
FeatureField Feature
sourceAccessions
ReferenceField Reference
sourceUri
ReferenceField Reference
spark
ADAMContext
sparkContextToADAMContext
ADAMContext
species
SequenceRecord ReferenceField Reference
splitFromMultiAllelic
GenotypeField VariantField Genotype Variant
sql
adam
start
Coverage MdTag ReferenceRegion AlignmentField FeatureField GenotypeField SliceField VariantField GenomicRegionPartitioner Alignment Feature Genotype Slice Variant VariantContext
strand
ReferencePosition ReferenceRegion FeatureField SliceField Feature Slice
strandBiasComponents
DefaultHeaderLines GenotypeField Genotype
stranded
ReferenceRegion
stream
InputStreamWithDecoder
stringency
BEDOutFormatter GFF3OutFormatter GTFOutFormatter NarrowPeakOutFormatter AnySAMOutFormatter VCFOutFormatter IndexedFastaFile
stripIndex
SequenceRecord
stripIndices
SequenceDictionary
subtract
ReferenceRegion
successProbabilityToPhred
PhredUtils
supplementaryAlignment
AlignmentField Alignment
symbolMap
Alphabet
symbols
Alphabet DNAAlphabet