S3ByteAccess
io
S3FileLocator
io
SAMFileHeaderWritable
models
SAMRecordConverter
converters
SNAPPY
CompressionCodecEnum
SchemaVal
FieldEnumeration
SchemaValue
FieldEnumeration
SequenceDictionary
models
SequenceRecord
models
SequenceUtils
util
SerializableAWSCredentials
util
SerializableUnboundRecordFilter
filters
ServoTimer
instrumentation
SingleFastqInputFormat
io
SingleReadBucket
models
SingleReadBucketSerializer
models
SmithWaterman
smithwaterman
SmithWatermanConstantGapScoring
smithwaterman
SmithWatermanGapScoringFromFn
smithwaterman
SnpTable
models
SparkMetrics
instrumentation
StageIdTagKey
SparkMetrics
StageNameTagKey
SparkMetrics
StatisticsMap
GenotypesSummary
String
TagType
sample
RecordGroup
sampleDescription
GenotypeField
sampleFields
VCFLine
sampleId
FlatGenotypeField GenotypeField
sampleIndices
VCFLineParser
samples
VCFLine VCFLineParser
samtoolsCigar
RichAlignmentRecord
sc
ADAMContext NucleotideContigFragmentContext AlignmentRecordContext VariationContext
schema
SchemaVal FieldValue
schemaFields
ParquetSchemaType
schemaName
ParquetSchemaType
schemas
BaseQualityScores BucketComparisons CombinedComparisons DupeMismatch MapQualityScores MappedPosition OverMatched
scoringMatrix
SmithWaterman
sd
SAMFileHeaderWritable
search
DNAPrefixTrie
secondOfPair
AlignmentRecordField
secondaryMapped
SingleReadBucket
secretKey
CredentialsProperties
seqLengths
GenomicRegionPartitioner
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
slashDivided
FileLocator
smithwaterman
algorithms
sortFastqOutput
ADAMSaveAnyArgs
source
FeatureField
space
ObservationAccumulator ObservationTable
sparkContextToADAMContext
ADAMContext NucleotideContigFragmentContext
sparkContextToADAMFeaturesContext
FeaturesContext
sparkContextToGeneContext
GeneContext
sparkContextToVariationContext
VariationContext
species
SequenceRecord
splitBySamples
Rod
splitFromMultiAllelic
GenotypeField
splitRodsBySamples
RodRDDFunctions
stageId
TaskContext
start
ReferenceRegion ReferenceRegionWithOrientation AlignmentRecordField FeatureField MdTag
strand
CDS Exon Gene Transcript UTR FeatureField GeneFeatureRDD
strandChar
BaseFeature
stream
InputStreamWithDecoder
stringToList
VcfStringUtils
stringToQualitySanger
PileupTraversable
stringifyRange
IDRangeIndexEntry RangeIndexEntry
successProbability
QualityScore
successProbabilityToPhred
PhredUtils
suffix
TypePath
suffixSearch
DNAPrefixTrie
supplmentaryAlignment
AlignmentRecordField