S3ByteAccess
io
S3FileLocator
io
SAMFileHeaderWritable
models
SAMRecordConverter
converters
SNAPPY
CompressionCodecEnum
SchemaVal
FieldEnumeration
SchemaValue
FieldEnumeration
SequenceDictionary
models
SequenceRecord
models
SerializableAWSCredentials
util
SerializableUnboundRecordFilter
filters
ServoTimer
instrumentation
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
ADAMGenotypeField
sampleFields
VCFLine
sampleId
ADAMFlatGenotypeField ADAMGenotypeField
sampleIndices
VCFLineParser
samples
VCFLine VCFLineParser
samtoolsCigar
RichADAMRecord
schema
SchemaVal FieldValue
schemaFields
ParquetSchemaType
schemaName
ParquetSchemaType
schemas
BaseQualityScores BucketComparisons CombinedComparisons DupeMismatch MapQualityScores MappedPosition OverMatched
score
BEDFeature NarrowPeakFeature
scoringMatrix
SmithWaterman
search
DNAPrefixTrie
secondOfPair
ADAMRecordField
secondaryMapped
SingleReadBucket
secretKey
CredentialsProperties
seqLengths
GenomicRegionPartitioner
sequence
ADAMRecordField
sequenceDictionary
IntervalListReader
sequencingCenter
RecordGroup
serialization
adam
set
TargetSet ZippedTargetSet
setHeader
ADAMVCFOutputFormat
setToJavaSet
ADAMContext
shiftIndel
NormalizationUtils
siftPred
ADAMDatabaseVariantAnnotationField
siftScore
ADAMDatabaseVariantAnnotationField
siftScoreConverted
ADAMDatabaseVariantAnnotationField
signalValue
NarrowPeakFeature ADAMFeatureField
simpleNucleotides
GenotypesSummaryCounts
singleNucleotideVariantCount
GenotypesSummaryCounts
singleNucleotideVariantCounts
GenotypesSummaryCounts
singleReadBucketToReadBucket
ReadBucket
singleton
FlagStatMetrics
singletonCount
GenotypesSummary
size
DNAPrefixTrie InputStreamWithDecoder
slashDivided
FileLocator
smithwaterman
algorithms
source
ADAMFeatureField
space
ObservationAccumulator ObservationTable
sparkContextToADAMContext
ADAMContext
sparkContextToADAMFeaturesContext
ADAMFeaturesContext
sparkContextToADAMVariationContext
ADAMVariationContext
species
SequenceRecord
splitBySamples
ADAMRod
splitFromMultiAllelic
ADAMGenotypeField
stageId
TaskContext
start
BaseFeature ReferenceRegion ReferenceRegionWithOrientation ADAMFeatureField ADAMRecordField MdTag
strand
BEDFeature NarrowPeakFeature ADAMFeatureField
stream
InputStreamWithDecoder
stringToList
VcfStringUtils
stringToQualitySanger
PileupTraversable
stringifyRange
IDRangeIndexEntry RangeIndexEntry
successProbability
QualityScore
successProbabilityToPhred
PhredUtils
suffix
TypePath
suffixSearch
DNAPrefixTrie