BamTools::BgzfData Struct Reference

Detailed description

Definition at line 67 of file BGZF.h.

#include <BGZF.h>

Public Methods
	BgzfData (const uint32_t threads=uint32_t(-1))
	~BgzfData (void)
void	Close (void)
void	Open (const std::string &filename, const char *mode)
int	Read (char *data, const unsigned int dataLength)
int	ReadBlock (void)
bool	Seek (int64_t position)
int64_t	Tell (void)
unsigned int	Write (const char *data, const unsigned int dataLen)
int	DeflateBlock (int32_t id, const unsigned int blockSize)
int	DeflateBlocks (void)
void	FlushBlocks (void)
int	InflateBlock (const int &blockLength)

Static Public Methods
static bool	CheckBlockHeader (char *header)
static void	PackUnsignedInt (char *buffer, unsigned int value)
static void	PackUnsignedShort (char *buffer, unsigned short value)
static signed int	UnpackSignedInt (char *buffer)
static unsigned int	UnpackUnsignedInt (char *buffer)
static unsigned short	UnpackUnsignedShort (char *buffer)

Public Members
unsigned int	UncompressedBlockSize
unsigned int	CompressedBlockSize
unsigned int	BlockLength
unsigned int	BlockOffset
uint64_t	BlockAddress
bool	IsOpen
bool	IsWriteOnly
FILE *	Stream
char *	UncompressedBlock
char *	CompressedBlock
nvbio::AtomicInt32	BackgroundThreads
nvbio::AtomicInt32	ActiveThreads
volatile unsigned int	CurrentBlockSize
nvbio::AtomicInt32	WorkCounter
uint32_t	ThreadCount
int volatile *	BlockLengths
BgzfThread *	ThreadPool

Constructor & Destructor Documentation

BamTools::BgzfData::BgzfData

(

const uint32_t

threads = uint32_t(-1))

Definition at line 54 of file BGZF.cpp.

BamTools::BgzfData::~BgzfData

(

void

)

Definition at line 93 of file BGZF.cpp.

Member Function Documentation

bool BamTools::BgzfData::CheckBlockHeader ( char *  header)

inlinestatic

Definition at line 134 of file BGZF.h.

void BamTools::BgzfData::Close

(

void

)

Definition at line 108 of file BGZF.cpp.

int BamTools::BgzfData::DeflateBlock	(	int32_t	id,
		const unsigned int	blockSize
	)

Definition at line 166 of file BGZF.cpp.

int BamTools::BgzfData::DeflateBlocks

(

void

)

Definition at line 122 of file BGZF.cpp.

void BamTools::BgzfData::FlushBlocks

(

void

)

Definition at line 243 of file BGZF.cpp.

int BamTools::BgzfData::InflateBlock

(

const int &

blockLength)

Definition at line 266 of file BGZF.cpp.

void BamTools::BgzfData::Open	(	const std::string &	filename,
		const char *	mode
	)

Definition at line 299 of file BGZF.cpp.

void BamTools::BgzfData::PackUnsignedInt ( char *  buffer, unsigned int  value  )

inlinestatic

Definition at line 148 of file BGZF.h.

void BamTools::BgzfData::PackUnsignedShort ( char *  buffer, unsigned short  value  )

inlinestatic

Definition at line 157 of file BGZF.h.

int BamTools::BgzfData::Read	(	char *	data,
		const unsigned int	dataLength
	)

Definition at line 318 of file BGZF.cpp.

int BamTools::BgzfData::ReadBlock

(

void

)

Definition at line 351 of file BGZF.cpp.

bool BamTools::BgzfData::Seek

(

int64_t

position)

Definition at line 395 of file BGZF.cpp.

int64_t BamTools::BgzfData::Tell

(

void

)

Definition at line 411 of file BGZF.cpp.

signed int BamTools::BgzfData::UnpackSignedInt ( char *  buffer)

inlinestatic

Definition at line 164 of file BGZF.h.

unsigned int BamTools::BgzfData::UnpackUnsignedInt ( char *  buffer)

inlinestatic

Definition at line 176 of file BGZF.h.

unsigned short BamTools::BgzfData::UnpackUnsignedShort ( char *  buffer)

inlinestatic

Definition at line 188 of file BGZF.h.

unsigned int BamTools::BgzfData::Write	(	const char *	data,
		const unsigned int	dataLen
	)

Definition at line 416 of file BGZF.cpp.

Member Data Documentation

nvbio::AtomicInt32 BamTools::BgzfData::ActiveThreads

Definition at line 82 of file BGZF.h.

nvbio::AtomicInt32 BamTools::BgzfData::BackgroundThreads

Definition at line 81 of file BGZF.h.

uint64_t BamTools::BgzfData::BlockAddress

Definition at line 74 of file BGZF.h.

unsigned int BamTools::BgzfData::BlockLength

Definition at line 72 of file BGZF.h.

int volatile* BamTools::BgzfData::BlockLengths

Definition at line 86 of file BGZF.h.

unsigned int BamTools::BgzfData::BlockOffset

Definition at line 73 of file BGZF.h.

char* BamTools::BgzfData::CompressedBlock

Definition at line 79 of file BGZF.h.

unsigned int BamTools::BgzfData::CompressedBlockSize

Definition at line 71 of file BGZF.h.

volatile unsigned int BamTools::BgzfData::CurrentBlockSize

Definition at line 83 of file BGZF.h.

bool BamTools::BgzfData::IsOpen

Definition at line 75 of file BGZF.h.

bool BamTools::BgzfData::IsWriteOnly

Definition at line 76 of file BGZF.h.

FILE* BamTools::BgzfData::Stream

Definition at line 77 of file BGZF.h.

uint32_t BamTools::BgzfData::ThreadCount

Definition at line 85 of file BGZF.h.

BgzfThread* BamTools::BgzfData::ThreadPool

Definition at line 87 of file BGZF.h.

char* BamTools::BgzfData::UncompressedBlock

Definition at line 78 of file BGZF.h.

unsigned int BamTools::BgzfData::UncompressedBlockSize

Definition at line 70 of file BGZF.h.

nvbio::AtomicInt32 BamTools::BgzfData::WorkCounter

Definition at line 84 of file BGZF.h.

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

• E:/git/nvbio/contrib/bamtools/BGZF.h
• E:/git/nvbio/contrib/bamtools/BGZF.cpp