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
sample
RecordGroup RecordGroupField
sampleDescription
GenotypeField Genotype
sampleId
FeatureField GenotypeField SampleField Feature Genotype
samples
MultisampleGenomicDataset DatasetBoundCoverageRDD DatasetBoundFeatureRDD ParquetUnboundCoverageRDD ParquetUnboundFeatureRDD RDDBoundCoverageRDD RDDBoundFeatureRDD DatasetBoundGenotypeRDD DatasetBoundVariantContextRDD ParquetUnboundGenotypeRDD RDDBoundGenotypeRDD RDDBoundVariantContextRDD VCFInFormatter
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
AvroGenomicDataset GenericGenomicDataset GenomicDataset DatasetBoundNucleotideContigFragmentRDD CoverageRDD DatasetBoundFeatureRDD DatasetBoundFragmentRDD DatasetBoundAlignmentRecordRDD DatasetBoundGenotypeRDD DatasetBoundVariantRDD VariantContextRDD
saveAsPartitionedParquet
GenomicDataset
saveAsSam
AlignmentRecordRDD
saveAsSamString
AlignmentRecordRDD
saveAsUcscBed
FeatureRDD
saveAsVcf
VariantContextRDD
saveAvro
GenomicDataset
saveMetadata
AvroGenomicDataset AvroRecordGroupGenomicDataset GenomicDataset MultisampleAvroGenomicDataset FeatureRDD GenotypeRDD VariantContextRDD VariantRDD
savePartitionMap
AvroGenomicDataset
saveProcessingSteps
AvroRecordGroupGenomicDataset
saveRddAsParquet
AvroGenomicDataset
saveRecordGroups
AvroRecordGroupGenomicDataset
saveSamples
MultisampleGenomicDataset
saveSequences
GenomicDataset
saveVcfHeaders
GenotypeRDD VariantContextRDD 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
DatasetBoundGenericGenomicDataset GenomicDataset RDDBoundGenericGenomicDataset DatasetBoundNucleotideContigFragmentRDD ParquetUnboundNucleotideContigFragmentRDD RDDBoundNucleotideContigFragmentRDD DatasetBoundCoverageRDD DatasetBoundFeatureRDD ParquetUnboundCoverageRDD ParquetUnboundFeatureRDD RDDBoundCoverageRDD RDDBoundFeatureRDD DatasetBoundFragmentRDD ParquetUnboundFragmentRDD RDDBoundFragmentRDD DatasetBoundAlignmentRecordRDD ParquetUnboundAlignmentRecordRDD RDDBoundAlignmentRecordRDD DatasetBoundGenotypeRDD DatasetBoundVariantContextRDD DatasetBoundVariantRDD ParquetUnboundGenotypeRDD ParquetUnboundVariantRDD RDDBoundGenotypeRDD RDDBoundVariantContextRDD RDDBoundVariantRDD VCFInFormatter IndexedFastaFile ReferenceContigMap ReferenceFile TwoBitFile
sequencingCenter
RecordGroup RecordGroupField
serialization
adam
setNestAnnotationInGenotypesProperty
VariantContextConverter
shuffleRegionJoin
GenomicDataset
shuffleRegionJoinAndGroupByLeft
GenomicDataset
size
Alphabet RecordGroupDictionary SequenceDictionary InputStreamWithDecoder
slices
SliceField
smithwaterman
algorithms
somatic
DefaultHeaderLines VariantAnnotationField VariantAnnotation
sort
GenomicDataset
sortByReference
FeatureRDD
sortFastqOutput
ADAMSaveAnyArgs
sortLexicographically
GenomicDataset
sortReadsByReadName
AlignmentRecordRDD
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 VariantContext
strand
ReferencePosition ReferenceRegion FeatureField SliceField Feature
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