libStatGen Software  1
IndexBase Class Reference
Inheritance diagram for IndexBase:
Collaboration diagram for IndexBase:

List of all members.


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< ReferencemyRefs

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.

number of references

Definition at line 139 of file IndexBase.cpp.

    // Return the number of references.
virtual StatGenStatus::Status IndexBase::readIndex ( const char *  filename) [pure virtual]
filenamethe bam index file to be read.
the status of the read.

Implemented in Tabix, and BamIndex.

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