SBamIndexBinInfo Struct Reference

Search Toolkit Book for SBamIndexBinInfo

#include <sra/readers/bam/bamindex.hpp>

Inheritance diagram for SBamIndexBinInfo:

Collaboration diagram for SBamIndexBinInfo:

Public Member Functions
void	Read (CNcbiIstream &in, SBamIndexParams params)
const char *	Read (const char *buffer_ptr, const char *buffer_end, SBamIndexParams params)
COpenRange< TSeqPos >	GetSeqRange (SBamIndexParams params) const
CBGZFPos	GetStartFilePos () const
CBGZFPos	GetEndFilePos () const

Public Attributes
TBin	m_Bin
CBGZFPos	m_Overlap
vector< CBGZFRange >	m_Chunks

Additional Inherited Members
Public Types inherited from SBamIndexDefs
enum	ESearchMode { eSearchByOverlap , eSearchByStart }
enum	EIndexLevel : uint8_t { kMinLevel = 0 , kLevel0 = kMinLevel , kLevel1 = kLevel0+1 , kMaxLevel = kBAI_depth }
typedef uint32_t	TBin
typedef uint8_t	TIndexLevel
typedef uint8_t	TShift
Static Public Attributes inherited from SBamIndexDefs
static const TBin	kMaxBinNumber = 0
static const TIndexLevel	kMinBinIndexLevel = 0
static const TShift	kLevelStepBinShift = 3
static const TShift	kBAI_min_shift = 14
static const TIndexLevel	kBAI_depth = 5

Detailed Description

Definition at line 343 of file bamindex.hpp.

Member Function Documentation

GetEndFilePos()

CBGZFPos SBamIndexBinInfo::GetEndFilePos ( ) const

inline

Definition at line 365 of file bamindex.hpp.

References m_Chunks.

Referenced by SBamRangeBlock::ExpandData(), and SBamRangeBlock::InitData().

GetSeqRange()

COpenRange<TSeqPos> SBamIndexBinInfo::GetSeqRange ( SBamIndexParams  params ) const

inline

Definition at line 350 of file bamindex.hpp.

References SBamIndexParams::GetSeqRange(), and m_Bin.

Referenced by SBamIndexRefIndex::ProcessBin().

GetStartFilePos()

CBGZFPos SBamIndexBinInfo::GetStartFilePos ( ) const

inline

Definition at line 361 of file bamindex.hpp.

References m_Chunks.

Referenced by SBamRangeBlock::ExpandData(), SBamRangeBlock::InitData(), and PByStartFilePos::operator()().

Read() [1/2]

void SBamIndexBinInfo::Read	(	CNcbiIstream &	in,
		SBamIndexParams	params
	)

Definition at line 198 of file bamindex.cpp.

References in(), SBamIndexParams::is_CSI, m_Bin, m_Chunks, m_Overlap, s_ReadFilePos(), s_ReadFileRange(), s_ReadInt32(), and s_ReadUInt32().

Referenced by SBamIndexRefIndex::Read().

Read() [2/2]

const char * SBamIndexBinInfo::Read	(	const char *	buffer_ptr,
		const char *	buffer_end,
		SBamIndexParams	params
	)

Definition at line 218 of file bamindex.cpp.

References data, i, SBamIndexParams::is_CSI, m_Bin, m_Chunks, m_Overlap, SBamUtil::MakeUint4(), SBamUtil::MakeUint8(), and s_Read().

Member Data Documentation

m_Bin

TBin SBamIndexBinInfo::m_Bin

Definition at line 355 of file bamindex.hpp.

Referenced by GetSeqRange(), operator<(), SBamIndexRefIndex::ProcessBin(), Read(), and SBamIndexRefIndex::Read().

m_Chunks

vector<CBGZFRange> SBamIndexBinInfo::m_Chunks

Definition at line 359 of file bamindex.hpp.

Referenced by SBamRangeBlock::ExpandData(), GetEndFilePos(), GetStartFilePos(), SBamRangeBlock::InitData(), SBamIndexRefIndex::ProcessBin(), SBamIndexRefIndex::ProcessPseudoBin(), and Read().

m_Overlap

CBGZFPos SBamIndexBinInfo::m_Overlap

Definition at line 357 of file bamindex.hpp.

Referenced by Read().

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

• include/sra/readers/bam/bamindex.hpp
• src/sra/readers/bam/bamindex.cpp