CBamIndex Class Reference

Search Toolkit Book for CBamIndex

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

Inheritance diagram for CBamIndex:

Collaboration diagram for CBamIndex:

Public Types
typedef vector< SBamIndexRefIndex >	TRefs
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

Public Member Functions
	CBamIndex ()
	CBamIndex (const string &index_file_name)
	~CBamIndex ()
const string &	GetFileName () const
void	Read (const string &index_file_name)
void	Read (const char *buffer_ptr, size_t buffer_size)
void	Read (CNcbiIstream &in)
const TRefs &	GetRefs () const
size_t	GetRefCount () const
const SBamIndexRefIndex &	GetRef (size_t ref_index) const
void	SetLengthFromHeader (const CBamHeader &header)
CBGZFRange	GetTotalFileRange (size_t ref_index) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (const CBamHeader &header, const string &ref_name, const string &seq_id, const string &annot_name, TIndexLevel min_index_level, TIndexLevel max_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (const CBamHeader &header, const string &ref_name, const string &seq_id, const string &annot_name, EIndexLevel min_index_level, EIndexLevel max_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (const CBamHeader &header, const string &ref_name, const string &seq_id, const string &annot_name, TIndexLevel min_index_level=0) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (const CBamHeader &header, const string &ref_name, const string &seq_id, const string &annot_name, EIndexLevel min_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (const CBamHeader &header, const string &ref_name, const CSeq_id &seq_id, const string &annot_name, TIndexLevel min_index_level, TIndexLevel max_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (const CBamHeader &header, const string &ref_name, const CSeq_id &seq_id, const string &annot_name, EIndexLevel min_index_level, EIndexLevel max_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (const CBamHeader &header, const string &ref_name, const CSeq_id &seq_id, const string &annot_name, TIndexLevel min_index_level=0) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (const CBamHeader &header, const string &ref_name, const CSeq_id &seq_id, const string &annot_name, EIndexLevel min_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const string &seq_id, const string &annot_name, TIndexLevel min_index_level, TIndexLevel max_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const string &seq_id, const string &annot_name, EIndexLevel min_index_level, EIndexLevel max_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const string &seq_id, const string &annot_name, TIndexLevel min_index_level=0) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const string &seq_id, const string &annot_name, EIndexLevel min_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const CSeq_id &seq_id, const string &annot_name, TIndexLevel min_index_level, TIndexLevel max_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const CSeq_id &seq_id, const string &annot_name, EIndexLevel min_index_level, EIndexLevel max_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const CSeq_id &seq_id, const string &annot_name, TIndexLevel min_index_level=0) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const CSeq_id &seq_id, const string &annot_name, EIndexLevel min_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const string &seq_id, const string &annot_name, TSeqPos ref_length, TIndexLevel min_index_level, TIndexLevel max_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const string &seq_id, const string &annot_name, TSeqPos ref_length, EIndexLevel min_index_level, EIndexLevel max_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const string &seq_id, const string &annot_name, TSeqPos ref_length, TIndexLevel min_index_level=0) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const string &seq_id, const string &annot_name, TSeqPos ref_length, EIndexLevel min_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const CSeq_id &seq_id, const string &annot_name, TSeqPos ref_length, TIndexLevel min_index_level, TIndexLevel max_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const CSeq_id &seq_id, const string &annot_name, TSeqPos ref_length, EIndexLevel min_index_level, EIndexLevel max_index_level) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const CSeq_id &seq_id, const string &annot_name, TSeqPos ref_length, TIndexLevel min_index_level=0) const
CRef< CSeq_annot >	MakeEstimatedCoverageAnnot (size_t ref_index, const CSeq_id &seq_id, const string &annot_name, TSeqPos ref_length, EIndexLevel min_index_level) const
vector< uint64_t >	CollectEstimatedCoverage (size_t ref_index, TIndexLevel min_index_level, TIndexLevel max_index_level) const
vector< uint64_t >	CollectEstimatedCoverage (size_t ref_index, EIndexLevel min_index_level, EIndexLevel max_index_level) const
vector< uint64_t >	CollectEstimatedCoverage (size_t ref_index, TIndexLevel index_level) const
vector< uint64_t >	CollectEstimatedCoverage (size_t ref_index, EIndexLevel index_level) const
vector< uint64_t >	CollectEstimatedCoverage (size_t ref_index) const
vector< uint64_t >	EstimateDataSizeByAlnStartPos (size_t ref_index) const
pair< Uint8, double >	GetReadStatistics () const
Public Member Functions inherited from SBamIndexParams
constexpr TShift	GetMinLevelBinShift () const
constexpr TIndexLevel	GetMaxIndexLevel () const
constexpr TIndexLevel	ToIndexLevel (EIndexLevel level) const
constexpr TShift	GetLevelBinShift (TIndexLevel level) const
constexpr TShift	GetLevelBinShift (EIndexLevel level) const
constexpr TSeqPos	GetBinSize (TIndexLevel level) const
constexpr TSeqPos	GetBinSize (EIndexLevel level) const
constexpr TShift	GetMinBinShift () const
constexpr TSeqPos	GetMinBinSize () const
constexpr TSeqPos	GetMaxBinSize () const
constexpr TSeqPos	GetPageSize () const
constexpr TShift	GetPageShift () const
constexpr TBin	GetBinNumberBaseReversed (int reversed_level) const
constexpr TBin	GetBinNumberBase (int level) const
constexpr TBin	GetBinNumberBase (EIndexLevel level) const
constexpr TBin	GetMinBinNumberBase () const
constexpr TBin	GetFirstOverflowBin (TIndexLevel level=0) const
constexpr TBin	GetFirstBin (TIndexLevel level) const
constexpr TBin	GetLastBin (TIndexLevel level) const
constexpr TBin	GetPseudoBin () const
bool	IsOverflowBin (TBin bin, TIndexLevel level=0) const
bool	IsOverflowPos (TSeqPos pos) const
TBin	GetBinNumberOffset (TSeqPos pos, TIndexLevel level) const
TBin	GetBinNumberOffset (TSeqPos pos, EIndexLevel level) const
TBin	GetBinNumber (TSeqPos pos, TIndexLevel level) const
TBin	GetBinNumber (TSeqPos pos, EIndexLevel level) const
pair< TBin, TBin >	GetBinRange (COpenRange< TSeqPos > ref_range, TIndexLevel index_level) const
TBin	GetUpperBinNumber (TBin bin) const
TIndexLevel	Bin2IndexLevel (TBin bin) const
TIndexLevel	GetRangeIndexLevel (CRange< TSeqPos > range) const
bool	RangeIsOnMinBinIndexLevel (CRange< TSeqPos > range) const
COpenRange< TSeqPos >	GetSeqRange (TBin bin) const

Private Attributes
string	m_FileName
TRefs	m_Refs
Uint8	m_UnmappedCount
Uint8	m_TotalReadBytes
double	m_TotalReadSeconds

Additional Inherited Members
Public Attributes inherited from SBamIndexParams
bool	is_CSI
TShift	min_shift
TIndexLevel	depth
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 446 of file bamindex.hpp.

Member Typedef Documentation

TRefs

typedef vector<SBamIndexRefIndex> CBamIndex::TRefs

Definition at line 463 of file bamindex.hpp.

Constructor & Destructor Documentation

CBamIndex() [1/2]

CBamIndex::CBamIndex

(

)

Definition at line 1168 of file bamindex.cpp.

CBamIndex() [2/2]

CBamIndex::CBamIndex ( const string &  index_file_name )

explicit

Definition at line 1176 of file bamindex.cpp.

References Read().

~CBamIndex()

CBamIndex::~CBamIndex

(

)

Definition at line 1185 of file bamindex.cpp.

Member Function Documentation

CollectEstimatedCoverage() [1/5]

vector<uint64_t> CBamIndex::CollectEstimatedCoverage ( size_t  ref_index ) const

inline

Definition at line 739 of file bamindex.hpp.

References CollectEstimatedCoverage(), and SBamIndexParams::GetMaxIndexLevel().

CollectEstimatedCoverage() [2/5]

vector<uint64_t> CBamIndex::CollectEstimatedCoverage ( size_t  ref_index, EIndexLevel  index_level  ) const

inline

Definition at line 731 of file bamindex.hpp.

References CollectEstimatedCoverage(), and SBamIndexParams::ToIndexLevel().

CollectEstimatedCoverage() [3/5]

vector<uint64_t> CBamIndex::CollectEstimatedCoverage ( size_t  ref_index, EIndexLevel  min_index_level, EIndexLevel  max_index_level  ) const

inline

Definition at line 714 of file bamindex.hpp.

References CollectEstimatedCoverage(), and SBamIndexParams::ToIndexLevel().

CollectEstimatedCoverage() [4/5]

vector<uint64_t> CBamIndex::CollectEstimatedCoverage ( size_t  ref_index, TIndexLevel  index_level  ) const

inline

Definition at line 725 of file bamindex.hpp.

References CollectEstimatedCoverage().

CollectEstimatedCoverage() [5/5]

vector< uint64_t > CBamIndex::CollectEstimatedCoverage	(	size_t	ref_index,
		TIndexLevel	min_index_level,
		TIndexLevel	max_index_level
	)		const

Definition at line 1482 of file bamindex.cpp.

References SBamIndexRefIndex::CollectEstimatedCoverage(), and GetRef().

Referenced by CBam2Seq_graph::CollectEstimatedCoverage(), CollectEstimatedCoverage(), and MakeEstimatedCoverageAnnot().

EstimateDataSizeByAlnStartPos()

vector<uint64_t> CBamIndex::EstimateDataSizeByAlnStartPos ( size_t  ref_index ) const

inline

Definition at line 746 of file bamindex.hpp.

References SBamIndexRefIndex::EstimateDataSizeByAlnStartPos(), and GetRef().

GetFileName()

const string& CBamIndex::GetFileName ( void  ) const

inline

Definition at line 454 of file bamindex.hpp.

References m_FileName.

Referenced by CBamRawDb::GetIndexName().

GetReadStatistics()

pair<Uint8, double> CBamIndex::GetReadStatistics ( ) const

inline

Definition at line 751 of file bamindex.hpp.

References m_TotalReadBytes, and m_TotalReadSeconds.

Referenced by CBamRawDb::GetEstimatedSecondsPerByte(), and CBamRawDb::Open().

GetRef()

const SBamIndexRefIndex & CBamIndex::GetRef

(

size_t

ref_index

)

const

Definition at line 1363 of file bamindex.cpp.

References GetRefCount(), m_Refs, and NCBI_THROW.

Referenced by CBamFileRangeSet::AddRanges(), CollectEstimatedCoverage(), CBamRawDb::EstimateDataSizeByAlnStartPos(), EstimateDataSizeByAlnStartPos(), GetTotalFileRange(), and CBamRefSeqInfo::x_LoadRangesEstimated().

GetRefCount()

size_t CBamIndex::GetRefCount ( ) const

inline

Definition at line 468 of file bamindex.hpp.

References m_Refs.

Referenced by GetRef(), and SetLengthFromHeader().

GetRefs()

const TRefs& CBamIndex::GetRefs ( void  ) const

inline

Definition at line 464 of file bamindex.hpp.

References m_Refs.

GetTotalFileRange()

CBGZFRange CBamIndex::GetTotalFileRange

(

size_t

ref_index

)

const

Definition at line 1386 of file bamindex.cpp.

References b, and GetRef().

MakeEstimatedCoverageAnnot() [1/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( const CBamHeader &  header, const string &  ref_name, const CSeq_id &  seq_id, const string &  annot_name, EIndexLevel  min_index_level  ) const

inline

Definition at line 546 of file bamindex.hpp.

References MakeEstimatedCoverageAnnot(), and SBamIndexParams::ToIndexLevel().

MakeEstimatedCoverageAnnot() [2/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( const CBamHeader &  header, const string &  ref_name, const CSeq_id &  seq_id, const string &  annot_name, EIndexLevel  min_index_level, EIndexLevel  max_index_level  ) const

inline

Definition at line 524 of file bamindex.hpp.

References MakeEstimatedCoverageAnnot(), and SBamIndexParams::ToIndexLevel().

MakeEstimatedCoverageAnnot() [3/24]

CRef< CSeq_annot > CBamIndex::MakeEstimatedCoverageAnnot	(	const CBamHeader &	header,
		const string &	ref_name,
		const CSeq_id &	seq_id,
		const string &	annot_name,
		TIndexLevel	min_index_level,
		TIndexLevel	max_index_level
	)		const

Definition at line 1429 of file bamindex.cpp.

References CBamHeader::GetRefIndex(), CBamHeader::GetRefLength(), MakeEstimatedCoverageAnnot(), and NCBI_THROW_FMT.

MakeEstimatedCoverageAnnot() [4/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( const CBamHeader &  header, const string &  ref_name, const CSeq_id &  seq_id, const string &  annot_name, TIndexLevel  min_index_level = 0  ) const

inline

Definition at line 536 of file bamindex.hpp.

References SBamIndexParams::GetMaxIndexLevel(), and MakeEstimatedCoverageAnnot().

MakeEstimatedCoverageAnnot() [5/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( const CBamHeader &  header, const string &  ref_name, const string &  seq_id, const string &  annot_name, EIndexLevel  min_index_level  ) const

inline

Definition at line 507 of file bamindex.hpp.

References MakeEstimatedCoverageAnnot(), and SBamIndexParams::ToIndexLevel().

MakeEstimatedCoverageAnnot() [6/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( const CBamHeader &  header, const string &  ref_name, const string &  seq_id, const string &  annot_name, EIndexLevel  min_index_level, EIndexLevel  max_index_level  ) const

inline

Definition at line 485 of file bamindex.hpp.

References MakeEstimatedCoverageAnnot(), and SBamIndexParams::ToIndexLevel().

MakeEstimatedCoverageAnnot() [7/24]

CRef< CSeq_annot > CBamIndex::MakeEstimatedCoverageAnnot	(	const CBamHeader &	header,
		const string &	ref_name,
		const string &	seq_id,
		const string &	annot_name,
		TIndexLevel	min_index_level,
		TIndexLevel	max_index_level
	)		const

Definition at line 1416 of file bamindex.cpp.

Referenced by MakeEstimatedCoverageAnnot(), CBam2GraphApp::ProcessFile(), and CBam2GraphApp::ProcessSrz().

MakeEstimatedCoverageAnnot() [8/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( const CBamHeader &  header, const string &  ref_name, const string &  seq_id, const string &  annot_name, TIndexLevel  min_index_level = 0  ) const

inline

Definition at line 497 of file bamindex.hpp.

References SBamIndexParams::GetMaxIndexLevel(), and MakeEstimatedCoverageAnnot().

MakeEstimatedCoverageAnnot() [9/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( size_t  ref_index, const CSeq_id &  seq_id, const string &  annot_name, EIndexLevel  min_index_level  ) const

inline

Definition at line 619 of file bamindex.hpp.

References MakeEstimatedCoverageAnnot(), and SBamIndexParams::ToIndexLevel().

MakeEstimatedCoverageAnnot() [10/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( size_t  ref_index, const CSeq_id &  seq_id, const string &  annot_name, EIndexLevel  min_index_level, EIndexLevel  max_index_level  ) const

inline

Definition at line 599 of file bamindex.hpp.

References MakeEstimatedCoverageAnnot(), and SBamIndexParams::ToIndexLevel().

MakeEstimatedCoverageAnnot() [11/24]

CRef< CSeq_annot > CBamIndex::MakeEstimatedCoverageAnnot	(	size_t	ref_index,
		const CSeq_id &	seq_id,
		const string &	annot_name,
		TIndexLevel	min_index_level,
		TIndexLevel	max_index_level
	)		const

Definition at line 1471 of file bamindex.cpp.

References kInvalidSeqPos, and MakeEstimatedCoverageAnnot().

MakeEstimatedCoverageAnnot() [12/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( size_t  ref_index, const CSeq_id &  seq_id, const string &  annot_name, TIndexLevel  min_index_level = 0  ) const

inline

Definition at line 610 of file bamindex.hpp.

References SBamIndexParams::GetMaxIndexLevel(), and MakeEstimatedCoverageAnnot().

MakeEstimatedCoverageAnnot() [13/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( size_t  ref_index, const CSeq_id &  seq_id, const string &  annot_name, TSeqPos  ref_length, EIndexLevel  min_index_level  ) const

inline

Definition at line 697 of file bamindex.hpp.

References MakeEstimatedCoverageAnnot(), and SBamIndexParams::ToIndexLevel().

MakeEstimatedCoverageAnnot() [14/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( size_t  ref_index, const CSeq_id &  seq_id, const string &  annot_name, TSeqPos  ref_length, EIndexLevel  min_index_level, EIndexLevel  max_index_level  ) const

inline

Definition at line 675 of file bamindex.hpp.

References MakeEstimatedCoverageAnnot(), and SBamIndexParams::ToIndexLevel().

MakeEstimatedCoverageAnnot() [15/24]

CRef< CSeq_annot > CBamIndex::MakeEstimatedCoverageAnnot	(	size_t	ref_index,
		const CSeq_id &	seq_id,
		const string &	annot_name,
		TSeqPos	ref_length,
		TIndexLevel	min_index_level,
		TIndexLevel	max_index_level
	)		const

Definition at line 1491 of file bamindex.cpp.

References b, CollectEstimatedCoverage(), SBamIndexParams::GetBinSize(), i, kInvalidSeqPos, max(), min(), CSeq_graph_Base::SetA(), CByte_graph_Base::SetAxis(), CSeq_graph_Base::SetComp(), CSeq_annot_Base::SetData(), CSeq_graph_Base::SetGraph(), CSeq_graph_Base::SetLoc(), CByte_graph_Base::SetMax(), CByte_graph_Base::SetMin(), CSeq_graph_Base::SetNumval(), CByte_graph_Base::SetValues(), sx_SetTitle(), and uint32_t.

MakeEstimatedCoverageAnnot() [16/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( size_t  ref_index, const CSeq_id &  seq_id, const string &  annot_name, TSeqPos  ref_length, TIndexLevel  min_index_level = 0  ) const

inline

Definition at line 687 of file bamindex.hpp.

References SBamIndexParams::GetMaxIndexLevel(), and MakeEstimatedCoverageAnnot().

MakeEstimatedCoverageAnnot() [17/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( size_t  ref_index, const string &  seq_id, const string &  annot_name, EIndexLevel  min_index_level  ) const

inline

Definition at line 584 of file bamindex.hpp.

References MakeEstimatedCoverageAnnot(), and SBamIndexParams::ToIndexLevel().

MakeEstimatedCoverageAnnot() [18/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( size_t  ref_index, const string &  seq_id, const string &  annot_name, EIndexLevel  min_index_level, EIndexLevel  max_index_level  ) const

inline

Definition at line 564 of file bamindex.hpp.

References MakeEstimatedCoverageAnnot(), and SBamIndexParams::ToIndexLevel().

MakeEstimatedCoverageAnnot() [19/24]

CRef< CSeq_annot > CBamIndex::MakeEstimatedCoverageAnnot	(	size_t	ref_index,
		const string &	seq_id,
		const string &	annot_name,
		TIndexLevel	min_index_level,
		TIndexLevel	max_index_level
	)		const

Definition at line 1460 of file bamindex.cpp.

References kInvalidSeqPos, and MakeEstimatedCoverageAnnot().

MakeEstimatedCoverageAnnot() [20/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( size_t  ref_index, const string &  seq_id, const string &  annot_name, TIndexLevel  min_index_level = 0  ) const

inline

Definition at line 575 of file bamindex.hpp.

References SBamIndexParams::GetMaxIndexLevel(), and MakeEstimatedCoverageAnnot().

MakeEstimatedCoverageAnnot() [21/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( size_t  ref_index, const string &  seq_id, const string &  annot_name, TSeqPos  ref_length, EIndexLevel  min_index_level  ) const

inline

Definition at line 658 of file bamindex.hpp.

References MakeEstimatedCoverageAnnot(), and SBamIndexParams::ToIndexLevel().

MakeEstimatedCoverageAnnot() [22/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( size_t  ref_index, const string &  seq_id, const string &  annot_name, TSeqPos  ref_length, EIndexLevel  min_index_level, EIndexLevel  max_index_level  ) const

inline

Definition at line 636 of file bamindex.hpp.

References MakeEstimatedCoverageAnnot(), and SBamIndexParams::ToIndexLevel().

MakeEstimatedCoverageAnnot() [23/24]

CRef< CSeq_annot > CBamIndex::MakeEstimatedCoverageAnnot	(	size_t	ref_index,
		const string &	seq_id,
		const string &	annot_name,
		TSeqPos	ref_length,
		TIndexLevel	min_index_level,
		TIndexLevel	max_index_level
	)		const

Definition at line 1447 of file bamindex.cpp.

References MakeEstimatedCoverageAnnot().

MakeEstimatedCoverageAnnot() [24/24]

CRef<CSeq_annot> CBamIndex::MakeEstimatedCoverageAnnot ( size_t  ref_index, const string &  seq_id, const string &  annot_name, TSeqPos  ref_length, TIndexLevel  min_index_level = 0  ) const

inline

Definition at line 648 of file bamindex.hpp.

References SBamIndexParams::GetMaxIndexLevel(), and MakeEstimatedCoverageAnnot().

Read() [1/3]

void CBamIndex::Read

(

CNcbiIstream &

in

)

Definition at line 1250 of file bamindex.cpp.

References buf, SBamIndexParams::depth, ERR_POST, in(), SBamIndexParams::is_CSI, SBamIndexDefs::kBAI_depth, SBamIndexDefs::kBAI_min_shift, kIndexMagicBAI, kIndexMagicLength, m_Refs, m_UnmappedCount, min(), SBamIndexParams::min_shift, NCBI_THROW_FMT, NStr::PrintableString(), s_Read(), s_ReadInt32(), s_ReadUInt32(), s_ReadUInt64(), and Warning().

Read() [2/3]

void CBamIndex::Read	(	const char *	buffer_ptr,
		size_t	buffer_size
	)

Definition at line 1303 of file bamindex.cpp.

References buffer_size, SBamIndexParams::depth, ERR_POST, CZipCompression::fGZip, CCompressionStream::fOwnProcessor, CRWStreambuf::fOwnReader, i, SBamIndexParams::is_CSI, SBamIndexDefs::kBAI_depth, SBamIndexDefs::kBAI_min_shift, kGZipMagic, kGZipMagicLength, kIndexMagicBAI, kIndexMagicLength, m_Refs, m_UnmappedCount, SBamUtil::MakeUint4(), SBamUtil::MakeUint8(), SBamIndexParams::min_shift, NCBI_THROW_FMT, NStr::PrintableString(), Read(), s_Read(), and Warning().

Read() [3/3]

void CBamIndex::Read

(

const string &

index_file_name

)

Definition at line 1190 of file bamindex.cpp.

References data, CStopWatch::Elapsed(), CStopWatch::eStart, CBamDb::GetDebugLevel(), LOG_POST, m_FileName, m_Refs, m_TotalReadBytes, m_TotalReadSeconds, m_UnmappedCount, ReadVDBFile(), ncbi::grid::netcache::search::fields::size, and sw.

Referenced by CBamIndex(), CBamRawDb::Open(), CBam2GraphApp::ProcessSrz(), and Read().

SetLengthFromHeader()

void CBamIndex::SetLengthFromHeader

(

const CBamHeader &

header

)

Definition at line 1373 of file bamindex.cpp.

References CBamHeader::GetRef(), CBamHeader::GetRefCount(), GetRefCount(), i, SBamHeaderRefInfo::m_Length, m_Refs, and NCBI_THROW_FMT.

Referenced by CBamRawDb::Open().

Member Data Documentation

m_FileName

string CBamIndex::m_FileName

private

Definition at line 757 of file bamindex.hpp.

Referenced by GetFileName(), and Read().

m_Refs

TRefs CBamIndex::m_Refs

private

Definition at line 758 of file bamindex.hpp.

Referenced by GetRef(), GetRefCount(), GetRefs(), Read(), and SetLengthFromHeader().

m_TotalReadBytes

Uint8 CBamIndex::m_TotalReadBytes

private

Definition at line 760 of file bamindex.hpp.

Referenced by GetReadStatistics(), and Read().

m_TotalReadSeconds

double CBamIndex::m_TotalReadSeconds

private

Definition at line 761 of file bamindex.hpp.

Referenced by GetReadStatistics(), and Read().

m_UnmappedCount

Uint8 CBamIndex::m_UnmappedCount

private

Definition at line 759 of file bamindex.hpp.

Referenced by Read().

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

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