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Here is a list of all documented class members with links to the class documentation for each member:

### - s -

- SamCoordOutput() : SamCoordOutput
- SamFile() : SamFile
- SamFileHeader() : SamFileHeader
- SamFileReader() : SamFileReader
- SamFileWriter() : SamFileWriter
- SamHeaderRecord() : SamHeaderRecord
- SamHeaderRecordType : SamHeaderRecord
- SamRecord() : SamRecord
- SamRecordPool() : SamRecordPool
- SamReferenceInfo() : SamReferenceInfo
- SamValidationError() : SamValidationError
- SamValidationErrors() : SamValidationErrors
- SequenceTranslation : SamRecord
- seqWithEquals() : SamQuerySeqWithRef
- seqWithoutEquals() : SamQuerySeqWithRef
- Set() : CigarRoller
- set0BasedMatePosition() : SamRecord
- set0BasedPosition() : SamRecord
- set1BasedMatePosition() : SamRecord
- set1BasedPosition() : SamRecord
- setApplication() : GenomeSequence
- setAttemptRecovery() : InputFile
- setBaseMapType() : BaseAsciiMap, BaseComposition
- setBuffer() : SamRecord
- setBufferFromFile() : SamRecord
- setCigar() : SamRecord
- setDeletionIndel1() : GlfRecord
- setDeletionIndel2() : GlfRecord
- setDuplicate() : SamFlag
- setFields() : SamHeaderRecord
- setFlag() : SamRecord
- setHandlingType() : StatGenStatus
- setHDTag() : SamFileHeader
- setHeaderTextString() : GlfHeader
- setInsertionIndel1() : GlfRecord
- setInsertionIndel2() : GlfRecord
- setInsertSize() : SamRecord
- setLk() : GlfRecord
- setLkHet() : GlfRecord
- setLkHom1() : GlfRecord
- setLkHom2() : GlfRecord
- setMapQuality() : SamRecord
- setMateReferenceName() : SamRecord
- setMaxAllocatedRecs() : SamRecordPool
- setMaxErrors() : FastQFile
- setMinDepth() : GlfRecord
- setMinLk() : GlfRecord
- setName() : GlfRefSection
- setNotDuplicate() : SamFlag
- setNumPrimerBases() : BaseAsciiMap
- setOffset() : GlfRecord
- setOutputFile() : SamCoordOutput
- setPGTag() : SamFileHeader
- setProgressStream() : GenomeSequence
- setQuality() : SamRecord
- setQueryIndex() : SamSingleBaseMatchInfo
- setReadDepth() : GlfRecord
- SetReadFlags() : SamFile
- setReadName() : SamRecord
- SetReadSection() : SamFile
- SetReadSequenceTranslation() : SamFile
- setRecordType() : GlfRecord
- setRefBaseInt() : GlfRecord
- setReference() : PileupElement
- SetReference() : SamFile
- setReference() : SamRecord
- setReferenceName() : GenomeSequence, SamRecord
- setRefLen() : GlfRefSection
- setRGTag() : SamFileHeader
- setRmsMapQ() : GlfRecord
- setRtypeRef() : GlfRecord
- setSequence() : SamRecord
- setSequenceTranslation() : SamRecord
- setSortedValidation() : SamFile
- setSQTag() : SamFileHeader
- setStatus() : GlfStatus, StatGenStatus
- setTag() : SamHeaderRecord
- setType() : SamSingleBaseMatchInfo
- setUnmapped() : SamFlag
- SetWriteSequenceTranslation() : SamFile
- Severity : SamValidationError
- shiftIndelsLeft() : SamRecord
- size() : Cigar, ReusableVector< DATA_TYPE >
- skip : Cigar
- softClip : Cigar, SamFilter
- softClipBeginByRefPos() : CigarHelper
- softClipEndByRefPos() : CigarHelper
- SortedType : SamFile
- SPACE_TYPE : BaseAsciiMap
- SQ : SamHeaderRecord
- StatGenStatus() : StatGenStatus
- Status : FastQStatus, GlfStatus, StatGenStatus
- SUCCESS : GlfStatus, StatGenStatus
- sumMismatchQuality() : SamFilter