SAMInFormatter
read
SAMSave
Timers
SampleField
projections
SaveAsADAM
Timers
SaveAsVcf
Timers
SchemaVal
FieldEnumeration
SchemaValue
FieldEnumeration
ScoreAndMarkReads
Timers
SequenceDictionary
models
SequenceDictionaryReader
util
SequenceField
projections
SequenceRecord
models
ShuffleJoinAndGroupByLeft
Timers
ShuffleRegionJoin
rdd
SingleFastqInputFormat
io
SingleReadBucketSerializer
read
SliceField
projections
SmithWaterman
smithwaterman
SmithWatermanConstantGapScoring
smithwaterman
SnpTable
models
SortByIndex
Timers
SortReads
Timers
SortTargets
Timers
SortedIntervalPartitionJoinWithVictims
rdd
SortingRightSide
Timers
String
TagType
SweepReadOverReferenceForQuality
Timers
SweepReadsOverConsensus
Timers
Symbol
models
sameReferenceName
ReferenceRegion
sameStrand
ReferenceRegion
sameTypeConversionFn
ADAMContext
sample
RecordGroup RecordGroupField
sampleDescription
GenotypeField Genotype
sampleId
GenotypeField SampleField Genotype
samples
MultisampleGenomicRDD DatasetBoundGenotypeRDD ParquetUnboundGenotypeRDD RDDBoundGenotypeRDD VCFInFormatter VariantContextRDD
samtoolsCigar
RichAlignmentRecord
save
NucleotideContigFragmentRDD CoverageRDD FeatureRDD FragmentRDD AlignmentRecordRDD
saveAsBed
FeatureRDD
saveAsFasta
NucleotideContigFragmentRDD
saveAsFastq
AlignmentRecordRDD
saveAsGff3
FeatureRDD
saveAsGtf
FeatureRDD
saveAsIntervalList
FeatureRDD
saveAsNarrowPeak
FeatureRDD
saveAsPairedFastq
AlignmentRecordRDD
saveAsParquet
AvroGenomicRDD DatasetBoundNucleotideContigFragmentRDD DatasetBoundFeatureRDD DatasetBoundFragmentRDD DatasetBoundAlignmentRecordRDD DatasetBoundGenotypeRDD DatasetBoundVariantRDD
saveAsSam
AlignmentRecordRDD
saveAsSamString
AlignmentRecordRDD
saveAsVcf
VariantContextRDD
saveMetadata
AvroGenomicRDD AvroRecordGroupGenomicRDD MultisampleAvroGenomicRDD GenotypeRDD VariantRDD
savePartitionMap
AvroGenomicRDD
saveProcessingSteps
AvroRecordGroupGenomicRDD
saveRecordGroups
AvroRecordGroupGenomicRDD
saveSamples
MultisampleAvroGenomicRDD
saveSequences
AvroGenomicRDD
saveVcfHeaders
GenotypeRDD VariantRDD
sc
ADAMContext IndexedFastaFile
schema
SchemaVal FieldValue
score
FeatureField QualityScoreBin Feature
scoreFn
SmithWatermanConstantGapScoring
sd
ReferencePartitioner
secondaryAlignment
AlignmentRecordField AlignmentRecord
seqLengths
GenomeBins GenomicPositionPartitioner GenomicRegionPartitioner
sequence
AlignmentRecordField NucleotideContigFragmentField ReadField SequenceField SliceField AlignmentRecord NucleotideContigFragment
sequences
GenericGenomicRDD GenomicRDD DatasetBoundNucleotideContigFragmentRDD ParquetUnboundNucleotideContigFragmentRDD RDDBoundNucleotideContigFragmentRDD DatasetBoundCoverageRDD DatasetBoundFeatureRDD ParquetUnboundCoverageRDD ParquetUnboundFeatureRDD RDDBoundCoverageRDD RDDBoundFeatureRDD DatasetBoundFragmentRDD ParquetUnboundFragmentRDD RDDBoundFragmentRDD DatasetBoundAlignmentRecordRDD ParquetUnboundAlignmentRecordRDD RDDBoundAlignmentRecordRDD DatasetBoundGenotypeRDD DatasetBoundVariantRDD ParquetUnboundGenotypeRDD ParquetUnboundVariantRDD RDDBoundGenotypeRDD RDDBoundVariantRDD VCFInFormatter VariantContextRDD IndexedFastaFile ReferenceContigMap ReferenceFile TwoBitFile
sequencingCenter
RecordGroup RecordGroupField
serialization
adam
setNestAnnotationInGenotypesProperty
VariantContextConverter
shuffleRegionJoin
GenomicRDD
shuffleRegionJoinAndGroupByLeft
GenomicRDD
size
Alphabet RecordGroupDictionary SequenceDictionary InputStreamWithDecoder
slices
SliceField
smithwaterman
algorithms
somatic
DefaultHeaderLines VariantAnnotationField VariantAnnotation
sort
GenomicRDD
sortByReference
FeatureRDD
sortFastqOutput
ADAMSaveAnyArgs
sortLexicographically
GenomicRDD
sortReadsByReferencePosition
AlignmentRecordRDD
sortReadsByReferencePositionAndIndex
AlignmentRecordRDD
sorted
SequenceDictionary
source
FeatureField Feature
sparkContextToADAMContext
ADAMContext
species
SequenceRecord ContigField Contig
splitFromMultiAllelic
GenotypeField VariantField Genotype Variant
sql
adam
start
Coverage MdTag ReferenceRegion AlignmentRecordField FeatureField GenotypeField NucleotideContigFragmentField SliceField VariantField GenomicRegionPartitioner AlignmentRecord Feature Genotype NucleotideContigFragment Variant
strand
ReferencePosition ReferenceRegion FeatureField SliceField Feature
strandBiasComponents
DefaultHeaderLines GenotypeField Genotype
stranded
ReferenceRegion
stream
InputStreamWithDecoder
stringency
BEDOutFormatter GFF3OutFormatter GTFOutFormatter NarrowPeakOutFormatter AnySAMOutFormatter IndexedFastaFile
stripIndex
SequenceRecord
stripIndices
SequenceDictionary
subtract
ReferenceRegion
successProbabilityToPhred
PhredUtils
supplementaryAlignment
AlignmentRecordField AlignmentRecord
symbolMap
Alphabet
symbols
Alphabet DNAAlphabet