SBamIndexDefs Struct Reference

Search Toolkit Book for SBamIndexDefs

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

Inheritance diagram for SBamIndexDefs:

Public Types
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
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 114 of file bamindex.hpp.

Member Typedef Documentation

TBin

typedef uint32_t SBamIndexDefs::TBin

Definition at line 120 of file bamindex.hpp.

TIndexLevel

typedef uint8_t SBamIndexDefs::TIndexLevel

Definition at line 121 of file bamindex.hpp.

TShift

typedef uint8_t SBamIndexDefs::TShift

Definition at line 136 of file bamindex.hpp.

Member Enumeration Documentation

EIndexLevel

enum SBamIndexDefs::EIndexLevel : uint8_t

Enumerator
kMinLevel
kLevel0
kLevel1
kMaxLevel

Definition at line 141 of file bamindex.hpp.

ESearchMode

enum SBamIndexDefs::ESearchMode

Enumerator
eSearchByOverlap
eSearchByStart

Definition at line 116 of file bamindex.hpp.

Member Data Documentation

kBAI_depth

const TIndexLevel SBamIndexDefs::kBAI_depth = 5

static

Definition at line 139 of file bamindex.hpp.

Referenced by CBamIndex::Read().

kBAI_min_shift

const TShift SBamIndexDefs::kBAI_min_shift = 14

static

Definition at line 138 of file bamindex.hpp.

Referenced by CBamDb::GetPageSize(), and CBamIndex::Read().

kLevelStepBinShift

const TShift SBamIndexDefs::kLevelStepBinShift = 3

static

Definition at line 137 of file bamindex.hpp.

Referenced by SBamIndexParams::Bin2IndexLevel(), SBamIndexRefIndex::CollectEstimatedCoverage(), SBamIndexRefIndex::EstimateDataSizeByAlnStartPos(), SBamIndexRefIndex::GetAlnOverStarts(), SBamIndexParams::GetBinNumberBaseReversed(), SBamIndexParams::GetLevelBinShift(), SBamIndexParams::GetRangeIndexLevel(), SBamIndexParams::GetUpperBinNumber(), and SBamIndexRefIndex::ProcessBin().

kMaxBinNumber

const TBin SBamIndexDefs::kMaxBinNumber = 0

static

Definition at line 133 of file bamindex.hpp.

Referenced by SBamIndexParams::GetBinRange(), and s_GetSeqRange().

kMinBinIndexLevel

const TIndexLevel SBamIndexDefs::kMinBinIndexLevel = 0

static

Definition at line 134 of file bamindex.hpp.

Referenced by CBamFileRangeSet::AddRanges(), SBamIndexParams::GetBinRange(), SBamIndexParams::GetMinBinNumberBase(), SBamIndexParams::GetMinBinShift(), and SBamIndexParams::GetMinBinSize().

---

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

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