SAMFileHeaderWritable
models
SAMRecordConverter
converters
SAMSave
Timers
SEPARATOR
Flattener
SEQUENCE_COUNT_OFFSET
TwoBitFile
SEQ_RECORD_RESERVED_SIZE
TwoBitFile
SaveAsADAM
Timers
SchemaVal
FieldEnumeration
SchemaValue
FieldEnumeration
ScoreAndMarkReads
Timers
SequenceDictionary
models
SequenceOrderingByName
models
SequenceOrderingByRefIdx
models
SequenceRecord
models
ShuffleRegionJoin
rdd
SingleFastqInputFormat
io
SingleReadBucket
models
SingleReadBucketSerializer
models
SmithWaterman
smithwaterman
SmithWatermanConstantGapScoring
smithwaterman
SmithWatermanGapScoringFromFn
smithwaterman
SnpTable
models
SortReads
Timers
SortTargets
Timers
String
TagType
SweepReadOverReferenceForQuality
Timers
Symbol
models
sample
RecordGroup
sampleDescription
GenotypeField
sampleId
GenotypeField
samtools
htsjdk
samtoolsCigar
RichAlignmentRecord
saveAsFasta
NucleotideContigFragmentRDDFunctions
saveAsVcf
VariantContextRDDFunctions
sc
ADAMContext ADAMSequenceDictionaryRDDAggregator MDTagging
schema
SchemaVal FieldValue
scoringMatrix
SmithWaterman
sd
SAMFileHeaderWritable ReferencePartitioner ShuffleRegionJoin
secondOfPair
AlignmentRecordField
secondaryAlignment
AlignmentRecordField
secondaryMapped
SingleReadBucket
seqLengths
GenomeBins GenomicPositionPartitioner GenomicRegionPartitioner
seqRecords
TwoBitFile
sequence
AlignmentRecordField
sequenceDictionary
IntervalListReader
sequencingCenter
RecordGroup
serialization
adam
set
TargetSet ZippedTargetSet
setHeader
ADAMVCFOutputFormat
setRegion
BAMFilteredRecordReader
setToJavaSet
ADAMContext
setVars
IndexedBamInputFormat
shiftIndel
NormalizationUtils
siftPred
DatabaseVariantAnnotationField
siftScore
DatabaseVariantAnnotationField
siftScoreConverted
DatabaseVariantAnnotationField
singleReadBucketToReadBucket
ReadBucket
singleton
FlagStatMetrics
size
Alphabet InputStreamWithDecoder
sliding
PairingRDD
smithwaterman
algorithms
sortFastqOutput
ADAMSaveAnyArgs
source
FeatureField
space
ObservationAccumulator ObservationTable
sparkContextToADAMContext
ADAMContext
species
SequenceRecord
splitFromMultiAllelic
GenotypeField
start
ReferenceRegion AlignmentRecordField FeatureField VariantField GenomicRegionPartitioner MdTag
strand
CDS Exon Gene Transcript UTR FeatureField
stream
InputStreamWithDecoder
stringToList
VcfStringUtils
stringency
BAMFilteredRecordReader
successProbability
QualityScore
successProbabilityToPhred
PhredUtils
supplementaryAlignment
AlignmentRecordField
symbolMap
Alphabet
symbols
Alphabet DNAAlphabet