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NCBI C++ ToolKit: include/sra/readers/bam/bgzf.hpp Source File

1 #ifndef SRA__READER__BAM__BGZF__HPP 2 #define SRA__READER__BAM__BGZF__HPP 60 return m_FilePos

.load(memory_order_acquire);

97 #define USE_RANGE_CACHE 1 98 #ifdef USE_RANGE_CACHE 108

pair<Uint8, double> GetReadStatistics()

const

;

109 void

SetPreviousReadStatistics(

const

pair<Uint8, double>&

stats

);

111 size_t

GetNextPageSizePow2()

const

;

114 void

x_AddReadStatistics(

Uint8

bytes,

double

seconds);

144 virtual const char

* GetErrCodeString(

void

)

const override

;

329 return

m_File->GetReadStatistics();

333

m_File->SetPreviousReadStatistics(

stats

);

336

pair<Uint8, double> GetUncompressStatistics()

const

;

341 void

x_AddUncompressStatistics(

Uint8

bytes,

double

seconds);

379 return

m_Block? m_Block->GetDataSize(): 0;

383 return

m_Block? m_Block->GetFileBlockPos(): 0;

387 return

m_Block? m_Block->GetNextFileBlockPos(): 0;

391 return

m_ReadPos < GetBlockDataSize();

396 return CBGZFPos

(GetBlockFilePos(), m_ReadPos);

400 return CBGZFPos

(GetNextBlockFilePos(), 0);

404 if

( HaveBytesInBlock() ) {

408 return

GetNextBlockPos();

419 size_t

GetNextAvailableBytes();

423 if

( HaveBytesInBlock() ) {

424 return

GetPos() < m_EndPos;

426 return

HaveNextDataBlock();

430 bool

HaveNextDataBlock();

ostream & operator<<(ostream &out, const CBGZFPos &p)

pair< CBGZFPos, CBGZFPos > CBGZFRange

TFileBlockPos GetFileBlockPos() const

TFileBlockSize GetFileBlockSize() const

static const TDataSize kMaxDataSize

atomic< TFileBlockPos > m_FileBlockPos

static const TFileBlockSize kMaxFileBlockSize

TFileBlockSize m_FileBlockSize

TFileBlockPos GetNextFileBlockPos() const

TDataSize GetDataSize() const

@ eFormatError

includes decompression errors

NCBI_EXCEPTION_DEFAULT(CBGZFException, CException)

void SetPreviousReadStatistics(const pair< Uint8, double > &stats)

TBlockCache::CLock TBlock

pair< Uint8, double > GetReadStatistics() const

CBGZFPos::TFileBlockPos TFileBlockPos

Uint8 m_TotalUncompressBytes

CCacheWithLock< TFileBlockPos, CBGZFBlock > TBlockCache

CRef< CPagedFile > m_File

double m_TotalUncompressSeconds

CRef< TBlockCache > m_BlockCache

bool operator<=(const CBGZFPos &b) const

DECLARE_OPERATOR_BOOL(m_VirtualPos !=0)

static const Uint4 kMaxBlockSize

TByteOffset GetByteOffset() const

bool operator!=(const CBGZFPos &b) const

bool operator>(const CBGZFPos &b) const

bool operator>=(const CBGZFPos &b) const

CBGZFPos(TVirtualPos pos)

TVirtualPos GetVirtualPos() const

CBGZFPos(TFileBlockPos block_pos, TByteOffset byte_offset)

TFileBlockPos GetFileBlockPos() const

static CBGZFPos GetInvalid()

bool operator<(const CBGZFPos &b) const

bool operator==(const CBGZFPos &b) const

CBGZFPos GetNextBlockPos() const

CBGZFPos GetSeekPos() const

CBGZFBlock::TFileBlockPos GetNextBlockFilePos() const

CBGZFBlock::TDataSize GetBlockDataSize() const

bool x_ReadBlock(CBGZFPos::TFileBlockPos file_pos)

CBGZFPos GetEndPos() const

bool HaveNextAvailableBytes()

const char * x_Read(CBGZFPos::TFileBlockPos file_pos, size_t size, char *buffer)

bool HaveBytesInBlock() const

CBGZFPos::TByteOffset m_ReadPos

CBGZFFile::TBlock m_Block

CSimpleBufferT< char > m_OutReadBuffer

CBGZFBlock::TFileBlockPos GetBlockFilePos() const

CSimpleBufferT< char > m_InReadBuffer

Class for support low level input/output for files.

size_t GetPageSize() const

atomic< TFilePos > m_FilePos

const char * GetPagePtr() const

TFilePos GetFilePos() const

CMemoryFileMap * m_MemFile

CSimpleBufferT< char > m_Buffer

bool Contains(TFilePos file_pos) const

double m_PreviousReadSeconds

CBinaryRangeCacheWithLock< TFilePos, CPagedFilePage > TPageCache

AutoPtr< CMemoryFileMap > m_MemFile

CPagedFilePage::TFilePos TFilePos

Uint8 m_PreviousReadBytes

double m_TotalReadSeconds

CRef< TPageCache > m_PageCache

Include a standard set of the NCBI C++ Toolkit most basic headers.

std::ofstream out("events_result.xml")

main entry point for tests

EErrCode

Error types that an application can generate.

void Read(CObjectIStream &in, TObjectPtr object, const CTypeRef &type)

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint16_t Uint2

2-byte (16-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_BAMREAD_EXPORT

const struct ncbi::grid::netcache::search::fields::SIZE size

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static Uint8 MakeUint8(const char *buf)

static Uint4 MakeUint4(const char *buf)

static Uint2 MakeUint2(const char *buf)

static float MakeFloat(const char *buf)

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