BamTools 2.5.2
Public Types | Public Member Functions | List of all members
BamTools::BamIndex Class Referenceabstract

Provides methods for generating & loading BAM index files. More...

#include <BamIndex.h>

Public Types

enum  IndexType { BAMTOOLS = 0 , STANDARD }
 

Public Member Functions

 BamIndex (Internal::BamReaderPrivate *reader)
 
virtual ~BamIndex ()
 
virtual bool Create ()=0
 
std::string GetErrorString ()
 
virtual bool HasAlignments (const int &referenceID) const =0
 
virtual bool Jump (const BamTools::BamRegion &region, bool *hasAlignmentsInRegion)=0
 
virtual bool Load (const std::string &filename)=0
 
virtual BamIndex::IndexType Type () const =0
 

Detailed Description

Provides methods for generating & loading BAM index files.

This class straddles the line between public API and internal implementation detail. Most client code should never have to use this class directly.

It is exposed to the public API to allow advanced users to implement their own custom indexing schemes.

Member Enumeration Documentation

◆ IndexType

Enumerator
BAMTOOLS 
STANDARD 

Constructor & Destructor Documentation

◆ BamIndex()

BamTools::BamIndex::BamIndex ( Internal::BamReaderPrivate *  reader)
inline

◆ ~BamIndex()

virtual BamTools::BamIndex::~BamIndex ( )
inlinevirtual

Member Function Documentation

◆ Create()

virtual bool BamTools::BamIndex::Create ( )
pure virtual

◆ GetErrorString()

std::string BamTools::BamIndex::GetErrorString ( )
inline

◆ HasAlignments()

virtual bool BamTools::BamIndex::HasAlignments ( const int &  referenceID) const
pure virtual

◆ Jump()

virtual bool BamTools::BamIndex::Jump ( const BamTools::BamRegion region,
bool *  hasAlignmentsInRegion 
)
pure virtual

◆ Load()

virtual bool BamTools::BamIndex::Load ( const std::string &  filename)
pure virtual

◆ Type()

virtual BamIndex::IndexType BamTools::BamIndex::Type ( ) const
pure virtual

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