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

### - a -

- Add() : CigarRoller
- add() : NonOverlapRegionPos, NonOverlapRegions, SamCoordOutput, SamReferenceInfo
- addComment() : SamFileHeader
- addEntry() : PileupElement, PileupElementBaseQual
- addError() : GlfStatus, SamValidationErrors, StatGenStatus
- addHD() : SamFileHeader
- addHeader() : SamFileHeader
- addHeaderLine() : SamFileHeader
- addIntTag() : SamRecord
- addKey() : SamHeaderRecord
- addPG() : SamFileHeader
- addPosition() : PosList
- addRecordCopy() : SamFileHeader
- addRG() : SamFileHeader
- addSQ() : SamFileHeader
- addTag() : SamRecord
- Align() : GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex >
- analyze() : PileupElement, PileupElementBaseQual, TestPileupElement
- appendCommentLines() : SamFileHeader
- appendString() : SamHeaderRecord
- areEqual() : BaseUtilities