CBamDb Class Reference

Search Toolkit Book for CBamDb

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

Collaboration diagram for CBamDb:

Classes
class	ICollectPileupCallback
struct	SAADBImpl
struct	SPileupValues
struct	STagInfo

Public Types
enum	EUseAPI { eUseDefaultAPI , eUseAlignAccess , eUseRawIndex }
typedef vector< STagInfo >	TTagList

Public Member Functions
	CBamDb (void)
	CBamDb (const CBamMgr &mgr, const string &db_name, EUseAPI use_api=eUseDefaultAPI)
	CBamDb (const CBamMgr &mgr, const string &db_name, const string &idx_name, EUseAPI use_api=eUseDefaultAPI)
	DECLARE_OPERATOR_BOOL (m_AADB||m_RawDB)
bool	UsesAlignAccessDB () const
bool	UsesRawIndex () const
CBamRawDb &	GetRawDb ()
const string &	GetDbName (void) const
const string &	GetIndexName (void) const
TSeqPos	GetPageSize () const
void	SetIdMapper (IIdMapper *idmapper, EOwnership ownership)
IIdMapper *	GetIdMapper (void) const
const TTagList &	GetIncludedAlignTags () const
bool	IncludeAlignTag (CTempString tag)
bool	ExcludeAlignTag (CTempString tag)
CRef< CSeq_id >	GetRefSeq_id (const string &label) const
CRef< CSeq_id >	GetShortSeq_id (const string &str, bool external=false) const
TSeqPos	GetRefSeqLength (const string &str) const
string	GetHeaderText (void) const
size_t	CollectPileup (SPileupValues &values, const string &ref_id, CRange< TSeqPos > graph_range, ICollectPileupCallback *callback=0, SPileupValues::EIntronMode intron_mode=SPileupValues::eNoCountIntron, TSeqPos gap_to_intron_threshold=kInvalidSeqPos) const

Static Public Member Functions
static bool	UseRawIndex (EUseAPI use_api)
static int	GetDebugLevel ()

Private Types
typedef unordered_map< string, TSeqPos >	TRefSeqLengths
typedef unordered_map< string, CRef< CSeq_id > >	TRefSeqIds

Private Attributes
string	m_DbName
string	m_IndexName
AutoPtr< IIdMapper >	m_IdMapper
TTagList	m_IncludedAlignTags
AutoPtr< TRefSeqLengths >	m_RefSeqLengths
AutoPtr< TRefSeqIds >	m_RefSeqIds
CRef< SAADBImpl >	m_AADB
CRef< CObjectFor< CBamRawDb > >	m_RawDB

Friends
class	CBamRefSeqIterator
class	CBamAlignIterator

Detailed Description

Definition at line 186 of file bamread.hpp.

Member Typedef Documentation

TRefSeqIds

typedef unordered_map<string, CRef<CSeq_id> > CBamDb::TRefSeqIds

private

Definition at line 521 of file bamread.hpp.

TRefSeqLengths

typedef unordered_map<string, TSeqPos> CBamDb::TRefSeqLengths

private

Definition at line 519 of file bamread.hpp.

TTagList

typedef vector<STagInfo> CBamDb::TTagList

Definition at line 254 of file bamread.hpp.

Member Enumeration Documentation

EUseAPI

enum CBamDb::EUseAPI

Enumerator
eUseDefaultAPI
eUseAlignAccess
eUseRawIndex

Definition at line 189 of file bamread.hpp.

Constructor & Destructor Documentation

CBamDb() [1/3]

CBamDb::CBamDb ( void  )

inline

Definition at line 194 of file bamread.hpp.

CBamDb() [2/3]

CBamDb::CBamDb	(	const CBamMgr &	mgr,
		const string &	db_name,
		EUseAPI	use_api = eUseDefaultAPI
	)

Definition at line 950 of file bamread.cpp.

References m_AADB, m_RawDB, s_UpdateVDBRequestContext(), and UseRawIndex().

CBamDb() [3/3]

CBamDb::CBamDb	(	const CBamMgr &	mgr,
		const string &	db_name,
		const string &	idx_name,
		EUseAPI	use_api = eUseDefaultAPI
	)

Definition at line 965 of file bamread.cpp.

References CObjectFor< T >::GetData(), m_AADB, m_IndexName, m_RawDB, s_UpdateVDBRequestContext(), and UseRawIndex().

Member Function Documentation

CollectPileup()

size_t CBamDb::CollectPileup	(	SPileupValues &	values,
		const string &	ref_id,
		CRange< TSeqPos >	graph_range,
		ICollectPileupCallback *	callback = 0,
		SPileupValues::EIntronMode	intron_mode = SPileupValues::eNoCountIntron,
		TSeqPos	gap_to_intron_threshold = kInvalidSeqPos
	)		const

DECLARE_OPERATOR_BOOL()

CBamDb::DECLARE_OPERATOR_BOOL

(

m_AADB||

m_RawDB

)

ExcludeAlignTag()

bool CBamDb::ExcludeAlignTag

(

CTempString

tag

)

Definition at line 1640 of file bamread.cpp.

References m_IncludedAlignTags, NCBI_THROW_FMT, and tag.

GetDbName()

const string& CBamDb::GetDbName ( void  ) const

inline

Definition at line 225 of file bamread.hpp.

References m_DbName.

Referenced by CBam2Seq_graph::CollectEstimatedCoverage(), CBam2Seq_graph::CollectRawAccessCoverage(), and CBam2Seq_graph::MakeSeq_entry().

GetDebugLevel()

int CBamDb::GetDebugLevel ( void  )

static

Definition at line 389 of file bamread.cpp.

References DEBUG, NCBI_PARAM_TYPE, and rapidjson::value.

Referenced by CBamIndex::Read(), and s_VDBInit().

GetHeaderText()

string CBamDb::GetHeaderText

(

void

)

const

Definition at line 1048 of file bamread.cpp.

References file, CObjectFor< T >::GetData(), m_AADB, m_RawDB, NCBI_THROW2, s_UpdateVDBRequestContext(), ncbi::grid::netcache::search::fields::size, string, and UsesRawIndex().

GetIdMapper()

IIdMapper* CBamDb::GetIdMapper ( void  ) const

inline

Definition at line 240 of file bamread.hpp.

References AutoPtr< X, Del >::get(), and m_IdMapper.

Referenced by CBamRefSeqIterator::GetIdMapper(), CBamAlignIterator::GetIdMapper(), GetRefSeq_id(), and GetShortSeq_id().

GetIncludedAlignTags()

const TTagList& CBamDb::GetIncludedAlignTags ( ) const

inline

Definition at line 255 of file bamread.hpp.

References m_IncludedAlignTags.

Referenced by CBamAlignIterator::GetMatchAlign().

GetIndexName()

const string& CBamDb::GetIndexName ( void  ) const

inline

Definition at line 229 of file bamread.hpp.

References m_IndexName.

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

GetPageSize()

TSeqPos CBamDb::GetPageSize

(

void

)

const

Definition at line 983 of file bamread.cpp.

References CObjectFor< T >::GetData(), SBamIndexDefs::kBAI_min_shift, m_RawDB, and UsesRawIndex().

GetRawDb()

CBamRawDb& CBamDb::GetRawDb ( )

inline

Definition at line 220 of file bamread.hpp.

References m_RawDB.

Referenced by CBam2Seq_graph::CollectEstimatedCoverage(), CBam2Seq_graph::CollectRawAccessCoverage(), CBamRefSeqInfo::CreateChunks(), CBamRefSeqInfo::EstimateAlignLoadSeconds(), CBamRefSeqInfo::EstimatePileupLoadSeconds(), CBamRefSeqInfo::EstimateSeqLoadSeconds(), and CBamRefSeqInfo::x_LoadRangesEstimated().

GetRefSeq_id()

CRef< CSeq_id > CBamDb::GetRefSeq_id

(

const string &

label

)

const

Definition at line 995 of file bamread.cpp.

References DEFINE_STATIC_FAST_MUTEX(), GetIdMapper(), label, m_RefSeqIds, and sx_GetRefSeq_id().

Referenced by CBamAlignIterator::GetMatchAlign(), CBamRefSeqIterator::GetRefSeq_id(), CBamAlignIterator::GetRefSeq_id(), and CBamUILoadManager::x_GetBamRefSeqs().

GetRefSeqLength()

TSeqPos CBamDb::GetRefSeqLength

(

const string &

str

)

const

Definition at line 1023 of file bamread.cpp.

References DEFINE_STATIC_FAST_MUTEX(), kInvalidSeqPos, len, and m_RefSeqLengths.

Referenced by CBam2Seq_graph::CollectCoverage(), and CBamFileInfo::GetRefSeqLength().

GetShortSeq_id()

CRef< CSeq_id > CBamDb::GetShortSeq_id	(	const string &	str,
		bool	external = false
	)		const

Definition at line 1017 of file bamread.cpp.

References GetIdMapper(), str(), and sx_GetShortSeq_id().

IncludeAlignTag()

bool CBamDb::IncludeAlignTag

(

CTempString

tag

)

Definition at line 1622 of file bamread.cpp.

References info, m_IncludedAlignTags, NCBI_THROW_FMT, and tag.

Referenced by CBamFileInfo::x_Initialize().

SetIdMapper()

void CBamDb::SetIdMapper ( IIdMapper *  idmapper, EOwnership  ownership  )

inline

Definition at line 236 of file bamread.hpp.

References m_IdMapper, and AutoPtr< X, Del >::reset().

Referenced by CBamUtils::CreateCoverageGraphs(), CCreateCoverageTask::Execute(), CBamUILoadManager::x_GetBamRefSeqs(), and CBamFileInfo::x_Initialize().

UseRawIndex()

bool CBamDb::UseRawIndex ( EUseAPI  use_api )

static

Definition at line 401 of file bamread.cpp.

References eUseDefaultAPI, eUseRawIndex, NCBI_PARAM_TYPE, and rapidjson::value.

Referenced by CBamDb().

UsesAlignAccessDB()

bool CBamDb::UsesAlignAccessDB ( ) const

inline

Definition at line 212 of file bamread.hpp.

References m_AADB.

UsesRawIndex()

bool CBamDb::UsesRawIndex ( ) const

inline

Definition at line 216 of file bamread.hpp.

References m_RawDB.

Referenced by CBamAlignIterator::CBamAlignIterator(), CBamRefSeqIterator::CBamRefSeqIterator(), CBam2Seq_graph::CollectEstimatedCoverage(), CBam2Seq_graph::CollectRawAccessCoverage(), CBamRefSeqInfo::CreateChunks(), CBamRefSeqInfo::EstimateAlignLoadSeconds(), CBamRefSeqInfo::EstimatePileupLoadSeconds(), CBamRefSeqInfo::EstimateSeqLoadSeconds(), GetHeaderText(), GetPageSize(), CBamRefSeqInfo::LoadMainSplit(), CBamRefSeqInfo::x_AddSeqChunk(), CBamRefSeqInfo::x_LoadRangesCov(), and CBamRefSeqInfo::x_LoadRangesEstimated().

Friends And Related Function Documentation

CBamAlignIterator

friend class CBamAlignIterator

friend

Definition at line 504 of file bamread.hpp.

CBamRefSeqIterator

friend class CBamRefSeqIterator

friend

Definition at line 503 of file bamread.hpp.

Member Data Documentation

m_AADB

CRef<SAADBImpl> CBamDb::m_AADB

private

Definition at line 523 of file bamread.hpp.

Referenced by CBamAlignIterator::CBamAlignIterator(), CBamDb(), CBamRefSeqIterator::CBamRefSeqIterator(), GetHeaderText(), and UsesAlignAccessDB().

m_DbName

string CBamDb::m_DbName

private

Definition at line 515 of file bamread.hpp.

Referenced by GetDbName().

m_IdMapper

AutoPtr<IIdMapper> CBamDb::m_IdMapper

private

Definition at line 517 of file bamread.hpp.

Referenced by GetIdMapper(), and SetIdMapper().

m_IncludedAlignTags

TTagList CBamDb::m_IncludedAlignTags

private

Definition at line 518 of file bamread.hpp.

Referenced by ExcludeAlignTag(), GetIncludedAlignTags(), and IncludeAlignTag().

m_IndexName

string CBamDb::m_IndexName

private

Definition at line 516 of file bamread.hpp.

Referenced by CBamDb(), and GetIndexName().

m_RawDB

CRef< CObjectFor<CBamRawDb> > CBamDb::m_RawDB

private

Definition at line 524 of file bamread.hpp.

Referenced by CBamAlignIterator::CBamAlignIterator(), CBamDb(), CBamRefSeqIterator::CBamRefSeqIterator(), GetHeaderText(), GetPageSize(), GetRawDb(), and UsesRawIndex().

m_RefSeqIds

AutoPtr<TRefSeqIds> CBamDb::m_RefSeqIds

mutableprivate

Definition at line 522 of file bamread.hpp.

Referenced by GetRefSeq_id().

m_RefSeqLengths

AutoPtr<TRefSeqLengths> CBamDb::m_RefSeqLengths

mutableprivate

Definition at line 520 of file bamread.hpp.

Referenced by GetRefSeqLength().

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

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