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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:

BamTools | Contains all BamTools classes & methods
Algorithms | Provides convenient classes & methods for working with BAM data
Sort | Provides classes & methods related to sorting BamAlignments
ByName | Function object for comparing alignments by name
ByPosition | Function object for comparing alignments by position
ByTag | Function object for comparing alignments by tag value
Unsorted | Placeholder function object
BamAlignment | The main BAM alignment data structure
CigarOp | Represents a CIGAR alignment operation
RefData | Represents a reference sequence entry
BamRegion | Represents a sequential genomic region
CustomHeaderTag |
BamIndex | Provides methods for generating & loading BAM index files
BamMultiReader | Convenience class for reading multiple BAM files
BamReader | Provides read access to BAM files
BamWriter | Provides write access for generating BAM files
IBamIODevice |
SamHeader | Represents the SAM-formatted text header that is part of the BAM file header
SamProgram | Represents a SAM program record
SamProgramChain | Sorted container "chain" of SamProgram records
SamReadGroup | Represents a SAM read group entry
SamReadGroupDictionary | Container of SamReadGroup entries
SamSequence | Represents a SAM sequence entry
SamSequenceDictionary | Container of SamSequence entries