SAMFileHeaderWritable
models
SAMRecordConverter
converters
SAMSave
Timers
SEQUENCE_COUNT_OFFSET
TwoBitFile
SEQ_RECORD_RESERVED_SIZE
TwoBitFile
SaveAsADAM
Timers
SchemaVal
FieldEnumeration
SchemaValue
FieldEnumeration
ScoreAndMarkReads
Timers
SequenceDictionary
models
SequenceRecord
models
SequenceUtils
util
ShuffleRegionJoin
rdd
SingleFastqInputFormat
io
SingleReadBucket
models
SingleReadBucketSerializer
models
SmithWaterman
smithwaterman
SmithWatermanConstantGapScoring
smithwaterman
SmithWatermanGapScoringFromFn
smithwaterman
SnpTable
models
SortReads
Timers
SortTargets
Timers
StatisticsMap
GenotypesSummary
String
TagType
SweepReadOverReferenceForQuality
Timers
sample
RecordGroup
sampleDescription
GenotypeField
sampleId
GenotypeField
samtoolsCigar
RichAlignmentRecord
sc
ADAMContext
schema
SchemaVal FieldValue
schemas
BaseQualityScores BucketComparisons CombinedComparisons DupeMismatch MapQualityScores MappedPosition OverMatched
scoringMatrix
SmithWaterman
sd
SAMFileHeaderWritable
search
DNAPrefixTrie
secondOfPair
AlignmentRecordField
secondaryMapped
SingleReadBucket
seqLengths
GenomeBins GenomicPositionPartitioner GenomicRegionPartitioner
seqRecords
TwoBitFile
sequence
AlignmentRecordField
sequenceDictionary
IntervalListReader
sequencingCenter
RecordGroup
serialization
adam
set
TargetSet ZippedTargetSet
setHeader
ADAMVCFOutputFormat
setToJavaSet
ADAMContext
shiftIndel
NormalizationUtils
siftPred
DatabaseVariantAnnotationField
siftScore
DatabaseVariantAnnotationField
siftScoreConverted
DatabaseVariantAnnotationField
simpleNucleotides
GenotypesSummaryCounts
singleNucleotideVariantCount
GenotypesSummaryCounts
singleNucleotideVariantCounts
GenotypesSummaryCounts
singleReadBucketToReadBucket
ReadBucket
singleton
FlagStatMetrics
singletonCount
GenotypesSummary
size
DNAPrefixTrie InputStreamWithDecoder
sliding
PairingRDD
smithwaterman
algorithms
sortFastqOutput
ADAMSaveAnyArgs
source
FeatureField
space
ObservationAccumulator ObservationTable
sparkContextToADAMContext
ADAMContext
species
SequenceRecord
splitBySamples
Rod
splitFromMultiAllelic
GenotypeField
splitRodsBySamples
RodRDDFunctions
start
ReferenceRegion ReferenceRegionWithOrientation AlignmentRecordField FeatureField GenomicRegionPartitioner MdTag
strand
CDS Exon Gene Transcript UTR FeatureField
strandChar
BaseFeature
stream
InputStreamWithDecoder
stringToList
VcfStringUtils
stringToQualitySanger
PileupTraversable
successProbability
QualityScore
successProbabilityToPhred
PhredUtils
suffixSearch
DNAPrefixTrie
supplmentaryAlignment
AlignmentRecordField