SAMInFormatter
read
SAMSave
Timers
SEPARATOR
Flattener
SampleField
projections
SaveAsADAM
Timers
SchemaVal
FieldEnumeration
SchemaValue
FieldEnumeration
ScoreAndMarkReads
Timers
SequenceDictionary
models
SequenceField
projections
SequenceRecord
models
ShuffleRegionJoin
rdd
SingleFastqInputFormat
io
SingleReadBucketSerializer
read
SliceField
projections
SmithWaterman
smithwaterman
SmithWatermanConstantGapScoring
smithwaterman
SnpTable
models
SortByIndex
Timers
SortReads
Timers
SortTargets
Timers
String
TagType
SweepReadOverReferenceForQuality
Timers
Symbol
models
sameTypeConversionFn
ADAMContext
sample
RecordGroup
RecordGroupMetadataField
sampleDescription
GenotypeField
sampleId
GenotypeField
SampleField
samples
MultisampleGenomicRDD
GenotypeRDD
VariantContextRDD
samtoolsCigar
RichAlignmentRecord
save
NucleotideContigFragmentRDD
CoverageRDD
FeatureRDD
FragmentRDD
AlignmentRecordRDD
GenotypeRDD
VariantAnnotationRDD
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
VariantRDD
sc
ADAMContext
FullOuterShuffleRegionJoin
InnerShuffleRegionJoin
InnerShuffleRegionJoinAndGroupByLeft
LeftOuterShuffleRegionJoin
RightOuterShuffleRegionJoin
RightOuterShuffleRegionJoinAndGroupByLeft
ShuffleRegionJoin
schema
SchemaVal
FieldValue
score
FeatureField
scoreFn
SmithWatermanConstantGapScoring
sd
FullOuterShuffleRegionJoin
InnerShuffleRegionJoin
InnerShuffleRegionJoinAndGroupByLeft
LeftOuterShuffleRegionJoin
ReferencePartitioner
RightOuterShuffleRegionJoin
RightOuterShuffleRegionJoinAndGroupByLeft
ShuffleRegionJoin
secondaryAlignment
AlignmentRecordField
seqLengths
GenomeBins
GenomicPositionPartitioner
GenomicRegionPartitioner
ShuffleRegionJoin
sequence
AlignmentRecordField
ReadField
SequenceField
SliceField
sequences
GenomicRDD
Unaligned
NucleotideContigFragmentRDD
CoverageRDD
FeatureRDD
FragmentRDD
AlignedReadRDD
GenotypeRDD
VariantAnnotationRDD
VariantContextRDD
VariantRDD
ReferenceContigMap
ReferenceFile
TwoBitFile
sequencingCenter
RecordGroup
RecordGroupMetadataField
serialization
adam
shuffleRegionJoin
GenomicRDD
shuffleRegionJoinAndGroupByLeft
GenomicRDD
size
Alphabet
InputStreamWithDecoder
smithwaterman
algorithms
somatic
VariantField
sort
GenomicRDD
sortByReference
FeatureRDD
sortFastqOutput
ADAMSaveAnyArgs
sortLexicographically
GenomicRDD
sortReadsByReferencePosition
AlignmentRecordRDD
sortReadsByReferencePositionAndIndex
AlignmentRecordRDD
sorted
SequenceDictionary
source
FeatureField
sparkContextToADAMContext
ADAMContext
species
SequenceRecord
ContigField
splitFromMultiAllelic
GenotypeField
start
Coverage
MdTag
ReferenceRegion
AlignmentRecordField
FeatureField
GenotypeField
SliceField
VariantField
GenomicRegionPartitioner
strand
FeatureField
SliceField
strandBiasComponents
GenotypeField
stream
InputStreamWithDecoder
stripIndex
SequenceRecord
stripIndices
SequenceDictionary
successProbabilityToPhred
PhredUtils
supplementaryAlignment
AlignmentRecordField
sweep
ShuffleRegionJoin
symbolMap
Alphabet
symbols
Alphabet
DNAAlphabet