Class for tracking the reference information mapping between the reference ids and the reference names. More...

#include <SamReferenceInfo.h>

Public Member Functions
	SamReferenceInfo ()
	Constructor.

	~SamReferenceInfo ()
	Destructor.

void	add (const char *referenceSequenceName, int32_t referenceSequenceLength)
	Add reference sequence name and reference sequence length.

int	getReferenceID (const String &referenceName, bool addID=false)
	Get the reference ID for the specified name, if addID is set to true, a reference id will be created for the referenceName if one does not already exist, while if addID is set to false (default), it will return NO_REF_ID if the reference name does not exist.

int	getReferenceID (const char *referenceName, bool addID=false)
	Get the reference ID for the specified name, if addID is set to true, a reference id will be created for the referenceName if one does not already exist, while if addID is set to false (default), it will return NO_REF_ID if the reference name does not exist.

const String &	getReferenceLabel (int id) const
	Get the reference name for the specified id, if the id is not found, return "*".

int32_t	getNumEntries () const
	Get the number of entries contained here.

const char *	getReferenceName (int index) const
	Return the reference name at the specified index, returning "" if the index is out of bounds.

int32_t	getReferenceLength (int index) const
	Return the reference length at the specified index, returning 0 if the index is out of bounds.

void	clear ()
	Reset this reference info.

SamReferenceInfo &	operator= (const SamReferenceInfo &rhs)
	Copy the reference information.

bool	operator== (const SamReferenceInfo &rhs) const

bool	operator!= (const SamReferenceInfo &rhs) const

Static Public Attributes
static const int	NO_REF_ID = -3
	Constant for the value returned if a reference id does not exist for a queried reference name.

Detailed Description

Class for tracking the reference information mapping between the reference ids and the reference names.

Definition at line 27 of file SamReferenceInfo.h.

The documentation for this class was generated from the following files:

bam/SamReferenceInfo.h
bam/SamReferenceInfo.cpp

Public Member Functions

Static Public Attributes

Detailed Description