NCBI C++ ToolKit
Public Member Functions | Public Attributes | List of all members
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< TSeqPosGetSeqRange (SBamIndexParams params) const
 
CBGZFPos GetStartFilePos () const
 
CBGZFPos GetEndFilePos () const
 

Public Attributes

TBin m_Bin
 
CBGZFPos m_Overlap
 
vector< CBGZFRangem_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

◆ Read() [1/2]

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

◆ Read() [2/2]

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

Member Data Documentation

◆ m_Bin

TBin SBamIndexBinInfo::m_Bin

◆ m_Chunks

vector<CBGZFRange> SBamIndexBinInfo::m_Chunks

◆ m_Overlap

CBGZFPos SBamIndexBinInfo::m_Overlap

Definition at line 357 of file bamindex.hpp.

Referenced by Read().


The documentation for this struct was generated from the following files:
Modified on Mon Apr 22 04:05:06 2024 by modify_doxy.py rev. 669887