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

- base2complement : BaseAsciiMap
- base2int : BaseAsciiMap
- baseColor2int : BaseAsciiMap
- baseNIndex : BaseAsciiMap
- baseXIndex : BaseAsciiMap
- color2int : BaseAsciiMap
- depth : glfEntry
- INDEX_NA : Cigar
- int2base : BaseAsciiMap
- int2colorSpace : BaseAsciiMap
- lk : glfEntry
- mapQuality : glfEntry
- myHasHeader : SamFile
- myIsBamOpenForRead : SamFile
- myIsOpenForRead : SamFile
- myIsOpenForWrite : SamFile
- myPrevCoord : SamFile
- myRecordCount : SamFile
- myStatistics : SamFile
- myStatus : SamFile
- NO_REF_ID : SamReferenceInfo
- offset : glfEntry
- REF_ID_ALL : BamIndex
- REF_ID_UNMAPPED : BamIndex
- refBase : glfEntry
- UNKNOWN_NUM_READS : BamIndex
- UNKNOWN_QUALITY_CHAR : BaseUtilities
- UNKNOWN_QUALITY_INT : BaseUtilities