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
RichAlignmentRecord
save
CoverageDataset FeatureDataset FragmentDataset AlignmentRecordDataset ReadDataset SequenceDataset SliceDataset
saveAsBed
FeatureDataset
saveAsFasta
SequenceDataset SliceDataset
saveAsFastq
AlignmentRecordDataset ReadDataset
saveAsGff3
FeatureDataset
saveAsGtf
FeatureDataset
saveAsIntervalList
FeatureDataset
saveAsNarrowPeak
FeatureDataset
saveAsPairedFastq
AlignmentRecordDataset
saveAsParquet
AvroGenomicDataset GenericGenomicDataset GenomicDataset CoverageDataset DatasetBoundFeatureDataset DatasetBoundFragmentDataset DatasetBoundAlignmentRecordDataset DatasetBoundReadDataset DatasetBoundSequenceDataset DatasetBoundSliceDataset DatasetBoundGenotypeDataset DatasetBoundVariantDataset VariantContextDataset
saveAsPartitionedParquet
GenomicDataset
saveAsSam
AlignmentRecordDataset
saveAsSamString
AlignmentRecordDataset
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
AlignmentRecordField AlignmentRecord
seqLengths
GenomeBins GenomicPositionPartitioner GenomicRegionPartitioner
sequence
AlignmentRecordField ReadField SequenceField SliceField rdd AlignmentRecord Read Sequence Slice
sequences
DatasetBoundGenericGenomicDataset GenomicDataset RDDBoundGenericGenomicDataset DatasetBoundCoverageDataset DatasetBoundFeatureDataset ParquetUnboundCoverageDataset ParquetUnboundFeatureDataset RDDBoundCoverageDataset RDDBoundFeatureDataset DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset DatasetBoundAlignmentRecordDataset DatasetBoundReadDataset ParquetUnboundAlignmentRecordDataset ParquetUnboundReadDataset RDDBoundAlignmentRecordDataset RDDBoundReadDataset DatasetBoundSequenceDataset DatasetBoundSliceDataset ParquetUnboundSequenceDataset ParquetUnboundSliceDataset RDDBoundSequenceDataset RDDBoundSliceDataset DatasetBoundGenotypeDataset DatasetBoundVariantContextDataset DatasetBoundVariantDataset ParquetUnboundGenotypeDataset ParquetUnboundVariantDataset RDDBoundGenotypeDataset RDDBoundVariantContextDataset RDDBoundVariantDataset VCFInFormatter IndexedFastaFile ReferenceContigMap ReferenceFile TwoBitFile
sequencesToAlignmentRecordsConversionFn
ADAMContext
sequencesToAlignmentRecordsDatasetConversionFn
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
slices
SliceField Slice
slicesToAlignmentRecordsConversionFn
ADAMContext
slicesToAlignmentRecordsDatasetConversionFn
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
AlignmentRecordDataset
sortByReference
FeatureDataset
sortByReferencePosition
AlignmentRecordDataset
sortByReferencePositionAndIndex
AlignmentRecordDataset
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 AlignmentRecordField FeatureField GenotypeField SliceField VariantField GenomicRegionPartitioner AlignmentRecord 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
AlignmentRecordField AlignmentRecord
symbolMap
Alphabet
symbols
Alphabet DNAAlphabet