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Here is a list of all functions with links to the classes they belong to:

### - s -

- SamHeader() : BamTools::SamHeader
- SamProgram() : BamTools::SamProgram
- SamProgramChain() : BamTools::SamProgramChain
- SamReadGroup() : BamTools::SamReadGroup
- SamReadGroupDictionary() : BamTools::SamReadGroupDictionary
- SamSequence() : BamTools::SamSequence
- SamSequenceDictionary() : BamTools::SamSequenceDictionary
- SaveAlignment() : BamTools::BamWriter
- Seek() : BamTools::IBamIODevice
- SetCompressionMode() : BamTools::BamWriter
- SetErrorString() : BamTools::IBamIODevice
- SetExplicitMergeOrder() : BamTools::BamMultiReader
- SetHeaderText() : BamTools::SamHeader
- SetIndex() : BamTools::BamReader
- SetIsDuplicate() : BamTools::BamAlignment
- SetIsFailedQC() : BamTools::BamAlignment
- SetIsFirstMate() : BamTools::BamAlignment
- SetIsMapped() : BamTools::BamAlignment
- SetIsMateMapped() : BamTools::BamAlignment
- SetIsMateReverseStrand() : BamTools::BamAlignment
- SetIsPaired() : BamTools::BamAlignment
- SetIsPrimaryAlignment() : BamTools::BamAlignment
- SetIsProperPair() : BamTools::BamAlignment
- SetIsReverseStrand() : BamTools::BamAlignment
- SetIsSecondMate() : BamTools::BamAlignment
- SetRegion() : BamTools::BamMultiReader, BamTools::BamReader
- Size() : BamTools::SamProgramChain, BamTools::SamReadGroupDictionary, BamTools::SamSequenceDictionary
- SortAlignments() : BamTools::Algorithms::Sort