BamTools::BamReader::BamReaderPrivate Struct Reference

Detailed description

Definition at line 26 of file BamReader.cpp.

Public Methods
	BamReaderPrivate (void)
	~BamReaderPrivate (void)
void	Close (void)
bool	Jump (int refID, int position=0)
void	Open (const string &filename, const string &indexFilename="")
bool	Rewind (void)
bool	GetNextAlignment (BamAlignment &bAlignment)
const string	GetHeaderText (void) const
const int	GetReferenceCount (void) const
const RefVector	GetReferenceData (void) const
const int	GetReferenceID (const string &refName) const
bool	CreateIndex (void)
int	BinsFromRegion (int refID, int left, uint16_t[MAX_BIN])
int	CalculateAlignmentEnd (const int &position, const std::vector< CigarOp > &cigarData)
int64_t	GetOffset (int refID, int left)
bool	IsOverlap (BamAlignment &bAlignment)
void	LoadHeaderData (void)
bool	LoadNextAlignment (BamAlignment &bAlignment)
void	LoadReferenceData (void)
bool	BuildIndex (void)
void	ClearIndex (void)
void	InsertBinEntry (BamBinMap &binMap, const uint32_t &saveBin, const uint64_t &saveOffset, const uint64_t &lastOffset)
void	InsertLinearOffset (LinearOffsetVector &offsets, const BamAlignment &bAlignment, const uint64_t &lastOffset)
bool	LoadIndex (void)
void	MergeChunks (void)
void	Roundup32 (int &value)
bool	WriteIndex (void)

Public Members
BgzfData	mBGZF
string	HeaderText
BamIndex	Index
RefVector	References
bool	IsIndexLoaded
int64_t	AlignmentsBeginOffset
string	Filename
string	IndexFilename
bool	IsRegionSpecified
int	CurrentRefID
int	CurrentLeft
const char *	DNA_LOOKUP
const char *	CIGAR_LOOKUP

Constructor & Destructor Documentation

BamTools::BamReader::BamReaderPrivate::BamReaderPrivate

(

void

)

Definition at line 158 of file BamReader.cpp.

BamTools::BamReader::BamReaderPrivate::~BamReaderPrivate

(

void

)

Definition at line 169 of file BamReader.cpp.

Member Function Documentation

int BamTools::BamReader::BamReaderPrivate::BinsFromRegion	(	int	refID,
		int	left,
		uint16_t	list[MAX_BIN]
	)

Definition at line 174 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::BuildIndex

(

void

)

Definition at line 197 of file BamReader.cpp.

int BamTools::BamReader::BamReaderPrivate::CalculateAlignmentEnd	(	const int &	position,
		const std::vector< CigarOp > &	cigarData
	)

Definition at line 327 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::ClearIndex

(

void

)

Definition at line 346 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::Close

(

void

)

Definition at line 351 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::CreateIndex

(

void

)

Definition at line 359 of file BamReader.cpp.

const string BamTools::BamReader::BamReaderPrivate::GetHeaderText

(

void

)

const

bool BamTools::BamReader::BamReaderPrivate::GetNextAlignment

(

BamAlignment &

bAlignment)

Definition at line 389 of file BamReader.cpp.

int64_t BamTools::BamReader::BamReaderPrivate::GetOffset	(	int	refID,
		int	left
	)

Definition at line 412 of file BamReader.cpp.

const int BamTools::BamReader::BamReaderPrivate::GetReferenceCount

(

void

)

const

const RefVector BamTools::BamReader::BamReaderPrivate::GetReferenceData

(

void

)

const

const int BamTools::BamReader::BamReaderPrivate::GetReferenceID

(

const string &

refName)

const

Definition at line 374 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::InsertBinEntry	(	BamBinMap &	binMap,
		const uint32_t &	saveBin,
		const uint64_t &	saveOffset,
		const uint64_t &	lastOffset
	)

Definition at line 457 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::InsertLinearOffset	(	LinearOffsetVector &	offsets,
		const BamAlignment &	bAlignment,
		const uint64_t &	lastOffset
	)

Definition at line 483 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::IsOverlap

(

BamAlignment &

bAlignment)

Definition at line 508 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::Jump	(	int	refID,
		int	position = 0
	)

Definition at line 521 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::LoadHeaderData

(

void

)

Definition at line 546 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::LoadIndex

(

void

)

Definition at line 574 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::LoadNextAlignment

(

BamAlignment &

bAlignment)

Definition at line 686 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::LoadReferenceData

(

void

)

Definition at line 819 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::MergeChunks

(

void

)

Definition at line 853 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::Open	(	const string &	filename,
		const string &	indexFilename = ""
	)

Definition at line 910 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::Rewind

(

void

)

Definition at line 930 of file BamReader.cpp.

void BamTools::BamReader::BamReaderPrivate::Roundup32

(

int &

value)

Definition at line 949 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::WriteIndex

(

void

)

Definition at line 960 of file BamReader.cpp.

Member Data Documentation

int64_t BamTools::BamReader::BamReaderPrivate::AlignmentsBeginOffset

Definition at line 38 of file BamReader.cpp.

const char* BamTools::BamReader::BamReaderPrivate::CIGAR_LOOKUP

Definition at line 49 of file BamReader.cpp.

int BamTools::BamReader::BamReaderPrivate::CurrentLeft

Definition at line 45 of file BamReader.cpp.

int BamTools::BamReader::BamReaderPrivate::CurrentRefID

Definition at line 44 of file BamReader.cpp.

const char* BamTools::BamReader::BamReaderPrivate::DNA_LOOKUP

Definition at line 48 of file BamReader.cpp.

string BamTools::BamReader::BamReaderPrivate::Filename

Definition at line 39 of file BamReader.cpp.

string BamTools::BamReader::BamReaderPrivate::HeaderText

Definition at line 34 of file BamReader.cpp.

BamIndex BamTools::BamReader::BamReaderPrivate::Index

Definition at line 35 of file BamReader.cpp.

string BamTools::BamReader::BamReaderPrivate::IndexFilename

Definition at line 40 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::IsIndexLoaded

Definition at line 37 of file BamReader.cpp.

bool BamTools::BamReader::BamReaderPrivate::IsRegionSpecified

Definition at line 43 of file BamReader.cpp.

BgzfData BamTools::BamReader::BamReaderPrivate::mBGZF

Definition at line 33 of file BamReader.cpp.

RefVector BamTools::BamReader::BamReaderPrivate::References

Definition at line 36 of file BamReader.cpp.

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

• E:/git/nvbio/contrib/bamtools/BamReader.cpp