SAMFileHeaderWritable
models
SAMInFormatter
read
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
SnpTable
models
SortByIndex
Timers
SortReads
Timers
SortTargets
Timers
String
TagType
SweepReadOverReferenceForQuality
Timers
Symbol
models
sameTypeConversionFn
ADAMContext
sample
RecordGroup
sampleDescription
GenotypeField
sampleId
GenotypeField
samples
MultisampleGenomicRDD GenotypeRDD VCFInFormatter VariantContextRDD
samtoolsCigar
RichAlignmentRecord
save
NucleotideContigFragmentRDD CoverageRDD FeatureRDD FragmentRDD AlignmentRecordRDD DatabaseVariantAnnotationRDD 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
saveMetadata
AvroGenomicRDD AvroReadGroupGenomicRDD MultisampleAvroGenomicRDD
sc
ADAMContext FullOuterShuffleRegionJoin InnerShuffleRegionJoin InnerShuffleRegionJoinAndGroupByLeft LeftOuterShuffleRegionJoin RightOuterShuffleRegionJoin RightOuterShuffleRegionJoinAndGroupByLeft ShuffleRegionJoin MDTagging
schema
SchemaVal FieldValue
score
FeatureField
scoreFn
SmithWatermanConstantGapScoring
sd
SAMFileHeaderWritable FullOuterShuffleRegionJoin InnerShuffleRegionJoin InnerShuffleRegionJoinAndGroupByLeft LeftOuterShuffleRegionJoin ReferencePartitioner RightOuterShuffleRegionJoin RightOuterShuffleRegionJoinAndGroupByLeft ShuffleRegionJoin
secondaryAlignment
AlignmentRecordField
secondaryMapped
SingleReadBucket
seqLengths
GenomeBins GenomicPositionPartitioner GenomicRegionPartitioner ShuffleRegionJoin
seqRecords
TwoBitFile
sequence
AlignmentRecordField
sequenceDictionary
IntervalListReader
sequences
GenomicRDD Unaligned NucleotideContigFragmentRDD CoverageRDD FeatureRDD FragmentRDD AlignedReadRDD DatabaseVariantAnnotationRDD GenotypeRDD VCFInFormatter VariantContextRDD VariantRDD ReferenceContigMap ReferenceFile TwoBitFile
sequencingCenter
RecordGroup
serialization
adam
set
TargetSet ZippedTargetSet
setIfNotEmpty
VariantAnnotations
shuffleRegionJoin
GenomicRDD
shuffleRegionJoinAndGroupByLeft
GenomicRDD
siftPred
DatabaseVariantAnnotationField
siftScore
DatabaseVariantAnnotationField
siftScoreConverted
DatabaseVariantAnnotationField
singleReadBucketToReadBucket
ReadBucket
singleton
FlagStatMetrics
size
Alphabet InputStreamWithDecoder
smithwaterman
algorithms
sortByReference
FeatureRDD
sortFastqOutput
ADAMSaveAnyArgs
sortReadsByReferencePosition
AlignmentRecordRDD
sortReadsByReferencePositionAndIndex
AlignmentRecordRDD
sorted
SequenceDictionary
source
FeatureField
space
ObservationAccumulator ObservationTable
sparkContextToADAMContext
ADAMContext
species
SequenceRecord
splitFromMultiAllelic
GenotypeField
start
Coverage ReferenceRegion AlignmentRecordField FeatureField GenotypeField VariantField GenomicRegionPartitioner MdTag
strand
FeatureField
stream
InputStreamWithDecoder
stripIndex
SequenceRecord
stripIndices
SequenceDictionary
successProbability
QualityScore
successProbabilityToPhred
PhredUtils
supplementaryAlignment
AlignmentRecordField
sweep
ShuffleRegionJoin
symbolMap
Alphabet
symbols
Alphabet DNAAlphabet