SAMInFormatter
read
SAMSave
Timers
SampleField
projections
SaveAsADAM
Timers
SchemaVal
FieldEnumeration
SchemaValue
FieldEnumeration
ScoreAndMarkReads
Timers
SequenceDictionary
models
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
SortingRightSide
Timers
String
TagType
SweepReadOverReferenceForQuality
Timers
Symbol
models
sameTypeConversionFn
ADAMContext
sample
RecordGroup RecordGroupMetadataField
sampleDescription
GenotypeField
sampleId
GenotypeField SampleField
samples
MultisampleGenomicRDD GenotypeRDD VCFInFormatter VariantContextRDD
samtoolsCigar
RichAlignmentRecord
save
NucleotideContigFragmentRDD CoverageRDD FeatureRDD FragmentRDD AlignmentRecordRDD GenotypeRDD VariantRDD
saveAsBed
FeatureRDD
saveAsFasta
NucleotideContigFragmentRDD
saveAsFastq
AlignmentRecordRDD
saveAsGff3
FeatureRDD
saveAsGtf
FeatureRDD
saveAsIntervalList
FeatureRDD
saveAsNarrowPeak
FeatureRDD
saveAsPairedFastq
AlignmentRecordRDD
saveAsParquet
AvroGenomicRDD
saveAsSam
AlignmentRecordRDD
saveAsSamString
AlignmentRecordRDD
saveAsVcf
GenotypeRDD VariantContextRDD VariantRDD
saveMetadata
AvroGenomicRDD AvroReadGroupGenomicRDD MultisampleAvroGenomicRDD VariantRDD
sc
ADAMContext FullOuterShuffleRegionJoin InnerShuffleRegionJoin InnerShuffleRegionJoinAndGroupByLeft LeftOuterShuffleRegionJoin RightOuterShuffleRegionJoin RightOuterShuffleRegionJoinAndGroupByLeft ShuffleRegionJoin IndexedFastaFile
schema
SchemaVal FieldValue
score
FeatureField
scoreFn
SmithWatermanConstantGapScoring
sd
FullOuterShuffleRegionJoin InnerShuffleRegionJoin InnerShuffleRegionJoinAndGroupByLeft LeftOuterShuffleRegionJoin ReferencePartitioner RightOuterShuffleRegionJoin RightOuterShuffleRegionJoinAndGroupByLeft ShuffleRegionJoin
secondaryAlignment
AlignmentRecordField
seqLengths
GenomeBins GenomicPositionPartitioner GenomicRegionPartitioner ShuffleRegionJoin
sequence
AlignmentRecordField ReadField SequenceField SliceField
sequences
GenomicRDD Unaligned NucleotideContigFragmentRDD CoverageRDD FeatureRDD FragmentRDD AlignmentRecordRDD GenotypeRDD VCFInFormatter VariantContextRDD VariantRDD IndexedFastaFile ReferenceContigMap ReferenceFile TwoBitFile
sequencingCenter
RecordGroup RecordGroupMetadataField
serialization
adam
shuffleRegionJoin
GenomicRDD
shuffleRegionJoinAndGroupByLeft
GenomicRDD
size
Alphabet InputStreamWithDecoder
smithwaterman
algorithms
somatic
DefaultHeaderLines VariantAnnotationField
sort
GenomicRDD
sortByReference
FeatureRDD
sortFastqOutput
ADAMSaveAnyArgs
sortLexicographically
GenomicRDD
sortReadsByReferencePosition
AlignmentRecordRDD
sortReadsByReferencePositionAndIndex
AlignmentRecordRDD
sorted
SequenceDictionary
source
FeatureField
sparkContextToADAMContext
ADAMContext
species
SequenceRecord ContigField
splitFromMultiAllelic
GenotypeField
start
Coverage MdTag ReferenceRegion AlignmentRecordField FeatureField GenotypeField SliceField VariantField GenomicRegionPartitioner
strand
ReferencePosition ReferenceRegion FeatureField SliceField
strandBiasComponents
DefaultHeaderLines GenotypeField
stranded
ReferenceRegion
stream
InputStreamWithDecoder
stringency
BEDOutFormatter GFF3OutFormatter GTFOutFormatter NarrowPeakOutFormatter IndexedFastaFile
stripIndex
SequenceRecord
stripIndices
SequenceDictionary
successProbabilityToPhred
PhredUtils
supplementaryAlignment
AlignmentRecordField
sweep
ShuffleRegionJoin
symbolMap
Alphabet
symbols
Alphabet DNAAlphabet