BamTools::BamIndex Class Reference

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

#include <BamIndex.h>

List of all members.

Public Types
enum	IndexType { BAMTOOLS = 0, STANDARD }
Public Member Functions
	BamIndex (Internal::BamReaderPrivate *reader)
virtual	~BamIndex (void)
virtual bool	Create (void)=0
std::string	GetErrorString (void)
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 (void) const =0

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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.

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Member Enumeration Documentation

enum BamTools::BamIndex::IndexType

Enumerator:

BAMTOOLS
STANDARD

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Constructor & Destructor Documentation

BamTools::BamIndex::BamIndex

(

Internal::BamReaderPrivate *

reader

)

[inline]

virtual BamTools::BamIndex::~BamIndex

(

void

)

[inline, virtual]

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Member Function Documentation

virtual bool BamTools::BamIndex::Create

(

void

)

[pure virtual]

std::string BamTools::BamIndex::GetErrorString

(

void

)

[inline]

virtual bool BamTools::BamIndex::HasAlignments

(

const int &

referenceID

)

const [pure virtual]

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

virtual bool BamTools::BamIndex::Load

(

const std::string &

filename

)

[pure virtual]

virtual BamIndex::IndexType BamTools::BamIndex::Type

(

void

)

const [pure virtual]

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

• BamIndex.h