bgzf.cpp File Reference

#include <ncbi_pch.hpp>
#include <sra/readers/bam/bgzf.hpp>
#include <util/util_exception.hpp>
#include <util/checksum.hpp>
#include <util/compress/zlib/zlib.h>

Include dependency graph for bgzf.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Enumerations
enum	EFileMode { eUseFileIO , eUseMemFile , eUseVDBFile }

Functions
	NCBI_PARAM_DECL (int, BGZF, DEBUG)
	NCBI_PARAM_DEF_EX (int, BGZF, DEBUG, 0, eParam_NoThread, BGZF_DEBUG)
static int	s_GetDebug (void)
static CPagedFile::TFilePos	s_GetPagePos (CPagedFile::TFilePos file_pos)
static char *	s_Reserve (size_t size, CSimpleBufferT< char > &buffer)
static const char *	s_Read (char *buffer, size_t len, CPagedFile &file, CPagedFile::TPage &page, Uint8 file_pos)
ostream &	operator<< (ostream &out, const CBGZFPos &p)
ostream &	operator<< (ostream &out, const CBGZFRange &r)

Variables
static const EFileMode	kFileMode = eUseVDBFile
static const bool	kCheckBlockCRC32 = true
static const size_t	kSegmentSizePow2 = 22
static const size_t	kSegmentSize = 1 << kSegmentSizePow2
static const size_t	kFixedHeaderSize = 12
static const size_t	kExtraHeaderSize = 4
static const size_t	kRequiredExtraSize = kExtraHeaderSize + 2
static const size_t	kInitialExtraSize = kRequiredExtraSize
static const size_t	kFooterSize = 8

Enumeration Type Documentation

EFileMode

enum EFileMode

Enumerator
eUseFileIO
eUseMemFile
eUseVDBFile

Definition at line 59 of file bgzf.cpp.

Function Documentation

NCBI_PARAM_DECL()

NCBI_PARAM_DECL	(	int	,
		BGZF	,
		DEBUG
	)

NCBI_PARAM_DEF_EX()

NCBI_PARAM_DEF_EX	(	int	,
		BGZF	,
		DEBUG	,
		0	,
		eParam_NoThread	,
		BGZF_DEBUG
	)

operator<<() [1/2]

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

Definition at line 337 of file bgzf.cpp.

References CBGZFPos::GetByteOffset(), CBGZFPos::GetFileBlockPos(), and out().

operator<<() [2/2]

ostream& operator<<	(	ostream &	out,
		const CBGZFRange &	r
	)

Definition at line 343 of file bgzf.cpp.

References out(), and r().

s_GetDebug()

static int s_GetDebug ( void  )

static

Definition at line 52 of file bgzf.cpp.

References DEBUG, NCBI_PARAM_TYPE, and rapidjson::value.

Referenced by CBGZFFile::x_ReadBlock(), CPagedFile::x_ReadPage(), CBGZFFile::~CBGZFFile(), and CPagedFile::~CPagedFile().

s_GetPagePos()

static CPagedFile::TFilePos s_GetPagePos ( CPagedFile::TFilePos  file_pos )

inlinestatic

Definition at line 77 of file bgzf.cpp.

References kSegmentSize.

Referenced by CPagedFile::GetPage().

s_Read()

static const char* s_Read ( char *  buffer, size_t  len, CPagedFile &  file, CPagedFile::TPage &  page, Uint8  file_pos  )

static

Definition at line 298 of file bgzf.cpp.

References _ASSERT, buffer, cnt, file, CBGZFBlock::kMaxFileBlockSize, len, and min().

Referenced by CBGZFFile::x_ReadBlock().

s_Reserve()

static char* s_Reserve ( size_t  size, CSimpleBufferT< char > &  buffer  )

inlinestatic

Definition at line 285 of file bgzf.cpp.

References buffer, max(), and ncbi::grid::netcache::search::fields::size.

Referenced by CSeq_graph::CReserveHook::PreReadChoiceVariant(), CSeqTable_multi_data::CReserveHook::PreReadChoiceVariant(), CDense_seg::CReserveHook::PreReadClassMember(), and CBGZFStream::Read().

Variable Documentation

kCheckBlockCRC32

const bool kCheckBlockCRC32 = true

static

Definition at line 65 of file bgzf.cpp.

Referenced by CBGZFFile::x_ReadBlock().

kExtraHeaderSize

const size_t kExtraHeaderSize = 4

static

Definition at line 479 of file bgzf.cpp.

Referenced by CBGZFFile::x_ReadBlock().

kFileMode

const EFileMode kFileMode = eUseVDBFile

static

Definition at line 64 of file bgzf.cpp.

Referenced by CPagedFile::CPagedFile().

kFixedHeaderSize

const size_t kFixedHeaderSize = 12

static

Definition at line 478 of file bgzf.cpp.

Referenced by CBGZFFile::x_ReadBlock().

kFooterSize

const size_t kFooterSize = 8

static

Definition at line 482 of file bgzf.cpp.

Referenced by CBGZFFile::x_ReadBlock().

kInitialExtraSize

const size_t kInitialExtraSize = kRequiredExtraSize

static

Definition at line 481 of file bgzf.cpp.

Referenced by CBGZFFile::x_ReadBlock().

kRequiredExtraSize

const size_t kRequiredExtraSize = kExtraHeaderSize + 2

static

Definition at line 480 of file bgzf.cpp.

Referenced by CBGZFFile::x_ReadBlock().

kSegmentSize

const size_t kSegmentSize = 1 << kSegmentSizePow2

static

Definition at line 74 of file bgzf.cpp.

Referenced by CPagedFile::GetPage(), and s_GetPagePos().

kSegmentSizePow2

const size_t kSegmentSizePow2 = 22

static

Definition at line 73 of file bgzf.cpp.