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

### - b -

- base2complement : BaseAsciiMap
- base2int : BaseAsciiMap
- baseColor2int : BaseAsciiMap
- baseNIndex : BaseAsciiMap
- baseXIndex : BaseAsciiMap

### - c -

- color2int : BaseAsciiMap

### - d -

- depth : glfEntry

### - e -

- elements : vector< T >

### - f -

- first_type : pair< T1, T2 >

### - i -

- INDEX_NA : Cigar
- int2base : BaseAsciiMap
- int2colorSpace : BaseAsciiMap

### - l -

- lk : glfEntry

### - m -

- mapQuality : glfEntry
- myHasHeader : SamFile
- myIsBamOpenForRead : SamFile
- myIsOpenForRead : SamFile
- myIsOpenForWrite : SamFile
- myPrevCoord : SamFile
- myRecordCount : SamFile
- myStatistics : SamFile
- myStatus : SamFile

### - n -

- NO_REF_ID : SamReferenceInfo

### - o -

- offset : glfEntry

### - r -

- REF_ID_ALL : BamIndex
- REF_ID_UNMAPPED : BamIndex
- refBase : glfEntry

### - s -

- second_type : pair< T1, T2 >

### - u -

- UNKNOWN_NUM_READS : BamIndex
- UNKNOWN_QUALITY_CHAR : BaseUtilities
- UNKNOWN_QUALITY_INT : BaseUtilities