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IndexBase Class Referenceabstract
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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. More...
 
bool getMinOffsetFromLinearIndex (int32_t refID, uint32_t position, uint64_t &minOffset) const
 

Static Protected Member Functions

static void getBinsForRegion (uint32_t start, uint32_t end, bool binMap[MAX_NUM_BINS+1])
 

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

◆ getNumRefs()

int32_t IndexBase::getNumRefs ( ) const

Get the number of references in this index.

Returns
number of references

Definition at line 139 of file IndexBase.cpp.

140 {
141  // Return the number of references.
142  return(myRefs.size());
143 }

◆ readIndex()

virtual StatGenStatus::Status IndexBase::readIndex ( const char *  filename)
pure virtual
Parameters
filenamethe bam index file to be read.
Returns
the status of the read.

Implemented in Tabix, and BamIndex.

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