Inheritance diagram for IndexBase:

Collaboration diagram for IndexBase:

Classes
class	Bin
class	Reference
Public Member Functions
virtual void	resetIndex ()
	Reset the member data for a new index file.
virtual StatGenStatus::Status	readIndex (const char *filename)=0
int32_t	getNumRefs () const
	Get the number of references in this index.
bool	getMinOffsetFromLinearIndex (int32_t refID, uint32_t position, uint64_t &minOffset) const
Static Protected Member Functions
static int	getBinsForRegion (uint32_t start, uint32_t end, uint16_t binList[MAX_NUM_BINS])
Protected Attributes
int32_t	n_ref
std::vector< Reference >	myRefs
Static Protected Attributes
static const uint32_t	MAX_NUM_BINS = 37450
static const uint32_t	MAX_POSITION = 536870911
static const uint32_t	LINEAR_INDEX_SHIFT = 14

Detailed Description

Definition at line 62 of file IndexBase.h.

Member Function Documentation

int32_t IndexBase::getNumRefs ( ) const

Get the number of references in this index.

Definition at line 139 of file IndexBase.cpp.

{
    // Return the number of references.
    return(myRefs.size());
}

virtual StatGenStatus::Status IndexBase::readIndex ( const char * filename ) [pure virtual]

Parameters:

filename the bam index file to be read.

Implemented in Tabix, and BamIndex.

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