Public Member Functions	BamAlignment (void)	constructor	BamAlignment (const BamAlignment &other)	copy constructor	~BamAlignment (void)	destructor
bool 	IsDuplicate (void) const
bool 	IsFailedQC (void) const
bool 	IsFirstMate (void) const
bool 	IsMapped (void) const
bool 	IsMateMapped (void) const
bool 	IsMateReverseStrand (void) const
bool 	IsPaired (void) const
bool 	IsPrimaryAlignment (void) const
bool 	IsProperPair (void) const
bool 	IsReverseStrand (void) const
bool 	IsSecondMate (void) const
void 	SetIsDuplicate (bool ok)	Sets value of "PCR duplicate" flag to ok.
void 	SetIsFailedQC (bool ok)	Sets "failed quality control" flag to ok.
void 	SetIsFirstMate (bool ok)	Sets "alignment is first mate" flag to ok.
void 	SetIsMapped (bool ok)	Sets "alignment is mapped" flag to ok.
void 	SetIsMateMapped (bool ok)	Sets "alignment's mate is mapped" flag to ok.
void 	SetIsMateReverseStrand (bool ok)	Sets "alignment's mate mapped to reverse strand" flag to ok.
void 	SetIsPaired (bool ok)	Sets "alignment part of paired-end read" flag to ok.
void 	SetIsPrimaryAlignment (bool ok)	Sets "position is primary alignment" flag to ok.
void 	SetIsProperPair (bool ok)	Sets "alignment is part of read that satisfied paired-end resolution" flag to ok.
void 	SetIsReverseStrand (bool ok)	Sets "alignment mapped to reverse strand" flag to ok.
void 	SetIsSecondMate (bool ok)	Sets "alignment is second mate on read" flag to ok.
void 	SetIsMateUnmapped (bool ok)	Complement of using SetIsMateMapped().
void 	SetIsSecondaryAlignment (bool ok)	Complement of using SetIsPrimaryAlignment().
void 	SetIsUnmapped (bool ok)	Complement of using SetIsMapped().
bool 	AddTag (const std::string &tag, const std::string &type, const std::string &value)	Adds a field with string data to the BAM tags.
bool 	AddTag (const std::string &tag, const std::string &type, const uint32_t &value)	Adds a field with unsigned integer data to the BAM tags.
bool 	AddTag (const std::string &tag, const std::string &type, const int32_t &value)	Adds a field with signed integer data to the BAM tags.
bool 	AddTag (const std::string &tag, const std::string &type, const float &value)	Adds a field with floating-point data to the BAM tags.
bool 	EditTag (const std::string &tag, const std::string &type, const std::string &value)	Edits a BAM tag field containing string data.
bool 	EditTag (const std::string &tag, const std::string &type, const uint32_t &value)	Edits a BAM tag field containing unsigned integer data.
bool 	EditTag (const std::string &tag, const std::string &type, const int32_t &value)	Edits a BAM tag field containing signed integer data.
bool 	EditTag (const std::string &tag, const std::string &type, const float &value)	Edits a BAM tag field containing floating-point data.
bool 	GetTag (const std::string &tag, std::string &destination) const	Retrieves the string value associated with a BAM tag.
bool 	GetTag (const std::string &tag, uint32_t &destination) const	Retrieves the unsigned integer value associated with a BAM tag.
bool 	GetTag (const std::string &tag, int32_t &destination) const	Retrieves the signed integer value associated with a BAM tag.
bool 	GetTag (const std::string &tag, float &destination) const	Retrieves the floating-point value associated with a BAM tag.
bool 	GetTagType (const std::string &tag, char &type) const	Retrieves the BAM tag type-code associated with requested tag name.
bool 	GetEditDistance (uint32_t &editDistance) const 	Retrieves value of edit distance tag ("NM").
bool 	GetReadGroup (std::string &readGroup) const 	Retrieves value of read group tag ("RG").
bool 	RemoveTag (const std::string &tag) 	Removes field from BAM tags.
bool 	BuildCharData (void) 	Populates alignment string fields (read name, bases, qualities, tag data).
int 	GetEndPosition (bool usePadded=false, bool zeroBased=true) const 	Calculates alignment end position, based on starting position and CIGAR data.