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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

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)

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 

Definition at line 148 of file BGZF.h.

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

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)

Definition at line 164 of file BGZF.h.

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

Definition at line 176 of file BGZF.h.

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

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.

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