CBamRefSeqInfo Class Reference

Search Toolkit Book for CBamRefSeqInfo

#include <sra/data_loaders/bam/impl/bamloader_impl.hpp>

Inheritance diagram for CBamRefSeqInfo:

Collaboration diagram for CBamRefSeqInfo:

Public Member Functions
	CBamRefSeqInfo (CBamFileInfo *bam_file, const string &refseqid, const CSeq_id_Handle &seq_id)
const string &	GetRefSeqId (void) const
const CSeq_id_Handle &	GetRefSeq_id (void) const
void	SetCovFileName (const string &name)
void	LoadRanges (void)
CRange< TSeqPos >	GetChunkGraphRange (size_t range_id)
void	LoadMainSplit (CTSE_LoadLock &load_lock)
void	LoadMainEntry (CTSE_LoadLock &load_lock)
void	CreateChunks (CTSE_Split_Info &split_info)
double	EstimateLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const
double	EstimatePileupLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const
double	EstimateAlignLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const
double	EstimateSeqLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const
void	LoadChunk (CTSE_Chunk_Info &chunk_info)
void	LoadMainChunk (CTSE_Chunk_Info &chunk_info)
void	LoadAlignChunk (CTSE_Chunk_Info &chunk_info)
void	LoadSeqChunk (CTSE_Chunk_Info &chunk_info)
void	LoadPileupChunk (CTSE_Chunk_Info &chunk_info)
void	GetShortSeqBlobId (CRef< CBAMBlobId > &ret, const CSeq_id_Handle &idh) const
void	SetBlobId (CRef< CBAMBlobId > &ret, const CSeq_id_Handle &idh) const
Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...
	CObject (const CObject &src)
	Copy constructor. More...
virtual	~CObject (void)
	Destructor. More...
CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...
bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...
bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...
bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...
bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...
void	AddReference (void) const
	Add reference to object. More...
void	RemoveReference (void) const
	Remove reference to object. More...
void	ReleaseReference (void) const
	Remove reference without deleting object. More...
virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...
virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...
void *	operator new (size_t size)
	Define new operator for memory allocation. More...
void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...
void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...
void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...
void *	operator new (size_t size, void *place)
	Define new operator. More...
void	operator delete (void *ptr, void *place)
	Define delete operator. More...
void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...
void	operator delete (void *ptr, CObjectMemoryPool *place)
	Define delete operator. More...
virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...
Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)
virtual	~CDebugDumpable (void)
void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void	DumpToConsole (void) const

Protected Types
typedef CRange< TSeqPos >	TRange
typedef vector< CBamRefSeqChunkInfo >	TChunks
typedef map< CSeq_id_Handle, int >	TSeq2Chunk

Protected Member Functions
void	x_LoadRangesScan (void)
void	x_LoadRangesStat (void)
bool	x_LoadRangesCov (void)
bool	x_LoadRangesEstimated (void)
void	x_InitAlignIterator (CBamAlignIterator &ait, TSeqPos &max_end_pos, CTSE_Chunk_Info &chunk_info, int base_id)
void	x_AddSeqChunk (CTSE_Chunk_Info &chunk_info, const vector< CSeq_id_Handle > &short_ids)
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes
CBamFileInfo *	m_File
string	m_RefSeqId
CSeq_id_Handle	m_RefSeq_id
string	m_CovFileName
CRef< CSeq_entry >	m_CovEntry
int	m_MinMapQuality
TChunks	m_Chunks
bool	m_LoadedRanges
CIRef< CBamAlignIterator::ISpotIdDetector >	m_SpotIdDetector
TSeq2Chunk	m_Seq2Chunk
CMutex	m_Seq2ChunkMutex

Additional Inherited Members
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...
typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...
typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...
typedef Uint8	TCount
	Alias for value type of counter. More...
Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)
static EAllocFillMode	GetAllocFillMode (void)
static void	SetAllocFillMode (EAllocFillMode mode)
static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...
Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)
Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...
static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...
static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...
static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...
static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Detailed Description

Definition at line 130 of file bamloader_impl.hpp.

Member Typedef Documentation

TChunks

typedef vector<CBamRefSeqChunkInfo> CBamRefSeqInfo::TChunks

protected

Definition at line 182 of file bamloader_impl.hpp.

TRange

typedef CRange<TSeqPos> CBamRefSeqInfo::TRange

protected

Definition at line 181 of file bamloader_impl.hpp.

TSeq2Chunk

typedef map<CSeq_id_Handle, int> CBamRefSeqInfo::TSeq2Chunk

protected

Definition at line 183 of file bamloader_impl.hpp.

Constructor & Destructor Documentation

CBamRefSeqInfo()

CBamRefSeqInfo::CBamRefSeqInfo	(	CBamFileInfo *	bam_file,
		const string &	refseqid,
		const CSeq_id_Handle &	seq_id
	)

Definition at line 868 of file bamloader_impl.cpp.

References m_SpotIdDetector.

Member Function Documentation

CreateChunks()

void CBamRefSeqInfo::CreateChunks

(

CTSE_Split_Info &

split_info

)

Definition at line 1602 of file bamloader_impl.cpp.

References _ASSERT, CTSE_Split_Info::AddChunk(), map_checker< Container >::clear(), CSeq_annot_Base::C_Data::e_Align, CSeq_annot_Base::C_Data::e_Graph, eChunk_align, eChunk_align1, eChunk_align2, eChunk_pileup_graph, SBamIndexDefs::eSearchByStart, CBamFileInfo::GetAnnotName(), CBamFileInfo::GetBamDb(), GetChunkGraphRange(), CTSE_Chunk_Info::GetChunkId(), GetDebugLevel(), CBamFileRangeSet::GetFileSize(), CBamRawDb::GetIndex(), GetPileupGraphsParam(), CBamDb::GetRawDb(), CBamRawDb::GetRefIndex(), GetRefSeq_id(), GetRefSeqId(), Info(), int, kChunkIdMul, SBamIndexDefs::kLevel0, SBamIndexDefs::kLevel1, kMax_UI4, SBamIndexDefs::kMaxLevel, kSingleAlignBytes, kSplitLevelsChunkDataSize, LOG_POST_X, m_Chunks, m_File, m_Seq2Chunk, m_Seq2ChunkMutex, PILEUP_NAME_SUFFIX, CBamDb::UsesRawIndex(), CTSE_Chunk_Info::x_AddAnnotType(), and CTSE_Chunk_Info::x_SetLoadBytes().

Referenced by LoadMainChunk(), and LoadMainEntry().

EstimateAlignLoadSeconds()

double CBamRefSeqInfo::EstimateAlignLoadSeconds	(	const CTSE_Chunk_Info &	chunk,
		Uint4	bytes
	)		const

Definition at line 1776 of file bamloader_impl.cpp.

References CBamFileInfo::GetBamDb(), CBamRawDb::GetEstimatedSecondsPerByte(), CBamDb::GetRawDb(), k_make_align_seconds, m_File, and CBamDb::UsesRawIndex().

Referenced by EstimateLoadSeconds().

EstimateLoadSeconds()

double CBamRefSeqInfo::EstimateLoadSeconds	(	const CTSE_Chunk_Info &	chunk,
		Uint4	bytes
	)		const

Definition at line 1812 of file bamloader_impl.cpp.

References eChunk_align, eChunk_align1, eChunk_align2, eChunk_pileup_graph, eChunk_short_seq, eChunk_short_seq1, eChunk_short_seq2, eChunk_short_seq_pileup, EstimateAlignLoadSeconds(), EstimatePileupLoadSeconds(), EstimateSeqLoadSeconds(), CTSE_Chunk_Info::GetChunkId(), and kChunkIdMul.

Referenced by CBAMDataLoader_Impl::EstimateLoadSeconds().

EstimatePileupLoadSeconds()

double CBamRefSeqInfo::EstimatePileupLoadSeconds	(	const CTSE_Chunk_Info &	chunk,
		Uint4	bytes
	)		const

Definition at line 1788 of file bamloader_impl.cpp.

References CBamFileInfo::GetBamDb(), CBamRawDb::GetEstimatedSecondsPerByte(), CBamDb::GetRawDb(), k_make_graph_seconds, m_File, and CBamDb::UsesRawIndex().

Referenced by EstimateLoadSeconds().

EstimateSeqLoadSeconds()

double CBamRefSeqInfo::EstimateSeqLoadSeconds	(	const CTSE_Chunk_Info &	chunk,
		Uint4	bytes
	)		const

Definition at line 1800 of file bamloader_impl.cpp.

References CBamFileInfo::GetBamDb(), CBamRawDb::GetEstimatedSecondsPerByte(), CBamDb::GetRawDb(), k_make_read_seconds, m_File, and CBamDb::UsesRawIndex().

Referenced by EstimateLoadSeconds().

GetChunkGraphRange()

CRange< TSeqPos > CBamRefSeqInfo::GetChunkGraphRange

(

size_t

range_id

)

Definition at line 1506 of file bamloader_impl.cpp.

References m_Chunks, and compile_time_bits::range().

Referenced by CreateChunks(), LoadPileupChunk(), and x_InitAlignIterator().

GetRefSeq_id()

const CSeq_id_Handle& CBamRefSeqInfo::GetRefSeq_id ( void  ) const

inline

Definition at line 141 of file bamloader_impl.hpp.

References m_RefSeq_id.

Referenced by CreateChunks(), LoadMainSplit(), LoadPileupChunk(), LoadRanges(), SetBlobId(), and x_LoadRangesEstimated().

GetRefSeqId()

const string& CBamRefSeqInfo::GetRefSeqId ( void  ) const

inline

Definition at line 137 of file bamloader_impl.hpp.

References m_RefSeqId.

Referenced by CreateChunks(), LoadAlignChunk(), LoadPileupChunk(), LoadRanges(), LoadSeqChunk(), x_AddSeqChunk(), x_InitAlignIterator(), x_LoadRangesEstimated(), x_LoadRangesScan(), and x_LoadRangesStat().

GetShortSeqBlobId()

void CBamRefSeqInfo::GetShortSeqBlobId	(	CRef< CBAMBlobId > &	ret,
		const CSeq_id_Handle &	idh
	)		const

Definition at line 896 of file bamloader_impl.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), m_Seq2Chunk, m_Seq2ChunkMutex, and SetBlobId().

LoadAlignChunk()

void CBamRefSeqInfo::LoadAlignChunk

(

CTSE_Chunk_Info &

chunk_info

)

Definition at line 1946 of file bamloader_impl.cpp.

References _ASSERT, _TRACE, eChunk_align, CStopWatch::Elapsed(), CStopWatch::eStart, CBamFileInfo::GetAnnotName(), CTSE_Chunk_Info::GetChunkId(), CBamAlignIterator::GetCIGARRefSize(), GetDebugLevel(), CSeq_id_Handle::GetHandle(), CBamAlignIterator::GetMapQuality(), CBamAlignIterator::GetMatchAlign(), GetRefSeqId(), CBamAlignIterator::GetRefSeqPos(), CBamAlignIterator::GetSeq_annot(), CBamAlignIterator::GetShortSeq_id(), CBamAlignIterator::GetShortSequenceLength(), Info(), kChunkIdMul, kInvalidSeqPos, kTSEId, LOG_POST_X, m_Chunks, m_File, m_MinMapQuality, s_AttachTime, s_CreateTime, CSeq_annot_Base::SetData(), CTSE_Chunk_Info::SetLoaded(), CStopWatch::Start(), CStopWatch::Stop(), sw, x_AddSeqChunk(), CTSE_Chunk_Info::x_AddUsedMemory(), x_InitAlignIterator(), and CTSE_Chunk_Info::x_LoadAnnot().

Referenced by LoadChunk().

LoadChunk()

void CBamRefSeqInfo::LoadChunk

(

CTSE_Chunk_Info &

chunk_info

)

Definition at line 1832 of file bamloader_impl.cpp.

References eChunk_align, eChunk_align1, eChunk_align2, eChunk_pileup_graph, eChunk_short_seq, eChunk_short_seq1, eChunk_short_seq2, eChunk_short_seq_pileup, CTSE_Chunk_Info::GetChunkId(), kChunkIdMul, kMainChunkId, LoadAlignChunk(), LoadMainChunk(), LoadPileupChunk(), and LoadSeqChunk().

LoadMainChunk()

void CBamRefSeqInfo::LoadMainChunk

(

CTSE_Chunk_Info &

chunk_info

)

Definition at line 1583 of file bamloader_impl.cpp.

References CreateChunks(), CSeq_entry::GetAnnot(), CTSE_Chunk_Info::GetSplitInfo(), ITERATE, kTSEId, LoadRanges(), m_CovEntry, CTSE_Chunk_Info::SetLoaded(), and CTSE_Chunk_Info::x_LoadAnnot().

Referenced by LoadChunk().

LoadMainEntry()

void CBamRefSeqInfo::LoadMainEntry

(

CTSE_LoadLock &

load_lock

)

Definition at line 1523 of file bamloader_impl.cpp.

References CreateChunks(), CSeq_entry::GetAnnot(), CTSE_Info::GetSplitInfo(), kTSEId, LoadRanges(), m_CovEntry, CBioseq_set_Base::SetAnnot(), CBioseq_set_Base::SetId(), CTSE_Info::SetSeq_entry(), and CSeq_entry_Base::SetSet().

LoadMainSplit()

void CBamRefSeqInfo::LoadMainSplit

(

CTSE_LoadLock &

load_lock

)

Definition at line 1536 of file bamloader_impl.cpp.

References CTSE_Split_Info::AddChunk(), CSeq_annot_Base::C_Data::e_Align, CSeq_annot_Base::C_Data::e_Graph, CStopWatch::Elapsed(), CBamFileInfo::GetAnnotName(), CBamFileInfo::GetBamDb(), GetDebugLevel(), GetEstimatedCoverageGraphParam(), GetPileupGraphsParam(), GetRefSeq_id(), CTSE_Info::GetSplitInfo(), COpenRange< Position >::GetWhole(), Info(), kMainChunkId, kTSEId, LOG_POST_X, m_CovEntry, m_CovFileName, m_File, PILEUP_NAME_SUFFIX, CBioseq_set_Base::SetId(), CTSE_Info::SetSeq_entry(), CSeq_entry_Base::SetSet(), CStopWatch::Start(), sw, CBamDb::UsesRawIndex(), and CTSE_Chunk_Info::x_AddAnnotType().

LoadPileupChunk()

void CBamRefSeqInfo::LoadPileupChunk

(

CTSE_Chunk_Info &

chunk_info

)

Definition at line 2844 of file bamloader_impl.cpp.

References _TRACE, SBaseStats::add_base(), SBaseStats::add_base_raw(), SBaseStats::add_gap(), SBaseStats::add_intron(), SBaseStats::add_match(), SBaseStats::cc, CTempString::data(), data, CStopWatch::Elapsed(), ERR_POST_X, SBaseStats::finish_add(), SBaseStats::get_max_count(), CBamFileInfo::GetAnnotName(), GetChunkGraphRange(), CTSE_Chunk_Info::GetChunkId(), CBamAlignIterator::GetCIGAR(), CBamAlignIterator::GetCIGARPos(), CBamAlignIterator::GetCIGARRefSize(), GetDebugLevel(), CRef< C, Locker >::GetNCPointer(), CBamAlignIterator::GetRawIndexIteratorPtr(), GetRefSeq_id(), GetRefSeqId(), CBamFileInfo::GetRefSeqLength(), CBamAlignIterator::GetRefSeqPos(), CBamRefSeqChunkInfo::GetRefSeqRange(), GetSeqId(), CBamAlignIterator::GetShortSequence(), GetSkipEmptyPileupGraphsParam(), i, Info(), kChunkIdMul, SBamAlignInfo::kCIGAR_D, SBamAlignInfo::kCIGAR_eq, SBamAlignInfo::kCIGAR_I, SBamAlignInfo::kCIGAR_M, SBamAlignInfo::kCIGAR_N, SBamAlignInfo::kCIGAR_S, SBamAlignInfo::kCIGAR_X, SBaseStats::kNumStat, SBaseStats::kStat_Intron, SBaseStats::kStat_Match, kTSEId, LOG_POST_X, m_Chunks, m_File, m_MinMapQuality, m_SpotIdDetector, max(), PILEUP_NAME_SUFFIX, SerialClone(), CSeq_annot_Base::SetData(), CSeq_annot_Base::SetDesc(), CSeq_interval_Base::SetFrom(), CSeq_graph_Base::SetGraph(), CSeq_interval_Base::SetId(), CTSE_Chunk_Info::SetLoaded(), CSeq_graph_Base::SetLoc(), CAnnotdesc_Base::SetName(), CSeq_graph_Base::SetNumval(), CBamAlignIterator::SetSpotIdDetector(), CSeq_graph_Base::SetTitle(), CSeq_interval_Base::SetTo(), CTempString::size(), CStopWatch::Start(), sw, sx_GetBaseRaw(), CTSE_Chunk_Info::x_AddUsedMemory(), and CTSE_Chunk_Info::x_LoadAnnot().

Referenced by LoadChunk().

LoadRanges()

void CBamRefSeqInfo::LoadRanges

(

void

)

Definition at line 990 of file bamloader_impl.cpp.

References _TRACE, GetRefSeq_id(), GetRefSeqId(), m_LoadedRanges, x_LoadRangesCov(), x_LoadRangesEstimated(), and x_LoadRangesStat().

Referenced by LoadMainChunk(), and LoadMainEntry().

LoadSeqChunk()

void CBamRefSeqInfo::LoadSeqChunk

(

CTSE_Chunk_Info &

chunk_info

)

Definition at line 2034 of file bamloader_impl.cpp.

References _ASSERT, _TRACE, eChunk_short_seq, eChunk_short_seq_pileup, CStopWatch::Elapsed(), map_checker< Container >::end(), CBamAlignIterator::eSearchByStart, map_checker< Container >::find(), CBamRefSeqChunkInfo::GetAlignStartRange(), CTSE_Chunk_Info::GetChunkId(), CBamAlignIterator::GetCIGARRefSize(), GetDebugLevel(), CSeq_id_Handle::GetHandle(), CBamAlignIterator::GetMapQuality(), CRef< C, Locker >::GetNCPointer(), GetRefSeqId(), CBamAlignIterator::GetRefSeqPos(), CBamRefSeqChunkInfo::GetRefSeqRange(), CBamAlignIterator::GetShortBioseq(), CBamAlignIterator::GetShortSeq_id(), CBamAlignIterator::GetShortSequenceLength(), i, Info(), set< Key, Compare >::insert(), kChunkIdMul, kInvalidSeqPos, SBamIndexDefs::kLevel0, kTSEId, LOG_POST_X, m_Chunks, m_File, m_MinMapQuality, CBamRefSeqChunkInfo::m_PileupChunkCount, m_Seq2Chunk, m_Seq2ChunkMutex, m_SpotIdDetector, CTSE_Chunk_Info::SetLoaded(), CBamAlignIterator::SetSpotIdDetector(), CStopWatch::Start(), sw, x_InitAlignIterator(), and CTSE_Chunk_Info::x_LoadBioseqs().

Referenced by LoadChunk().

SetBlobId()

void CBamRefSeqInfo::SetBlobId	(	CRef< CBAMBlobId > &	ret,
		const CSeq_id_Handle &	idh
	)		const

Definition at line 881 of file bamloader_impl.cpp.

References ERR_POST_X, CBamFileInfo::GetBamName(), GetRefSeq_id(), and m_File.

Referenced by GetShortSeqBlobId().

SetCovFileName()

void CBamRefSeqInfo::SetCovFileName ( const string &  name )

inline

Definition at line 146 of file bamloader_impl.hpp.

References m_CovFileName.

x_AddSeqChunk()

void CBamRefSeqInfo::x_AddSeqChunk ( CTSE_Chunk_Info &  chunk_info, const vector< CSeq_id_Handle > &  short_ids  )

protected

Definition at line 1900 of file bamloader_impl.cpp.

References _ASSERT, CTSE_Split_Info::AddChunk(), eChunk_align, eChunk_align2, eChunk_pileup_graph, eChunk_short_seq, CStopWatch::Elapsed(), first(), CBamFileInfo::GetBamDb(), CTSE_Chunk_Info::GetChunkId(), GetDebugLevel(), GetRefSeqId(), CTSE_Chunk_Info::GetSplitInfo(), Info(), map_checker< Container >::insert(), kChunkIdMul, kTSEId, LOG_POST_X, m_Chunks, m_File, m_Seq2Chunk, m_Seq2ChunkMutex, s_AttachTime, CStopWatch::Start(), CBamDb::UsesRawIndex(), CTSE_Chunk_Info::x_AddBioseqId(), CTSE_Chunk_Info::x_AddBioseqPlace(), and CTSE_Chunk_Info::x_SetLoadBytes().

Referenced by LoadAlignChunk().

x_InitAlignIterator()

void CBamRefSeqInfo::x_InitAlignIterator ( CBamAlignIterator &  ait, TSeqPos &  max_end_pos, CTSE_Chunk_Info &  chunk_info, int  base_id  )

protected

Definition at line 1857 of file bamloader_impl.cpp.

References _ASSERT, eChunk_align, eChunk_align1, eChunk_align2, eChunk_pileup_graph, CBamAlignIterator::eSearchByStart, GetChunkGraphRange(), CTSE_Chunk_Info::GetChunkId(), CRef< C, Locker >::GetNCPointer(), GetRefSeqId(), CBamFileInfo::GetRefSeqLength(), kChunkIdMul, kInvalidSeqPos, SBamIndexDefs::kLevel0, SBamIndexDefs::kLevel1, SBamIndexDefs::kMaxLevel, m_Chunks, m_File, m_SpotIdDetector, min(), and CBamAlignIterator::SetSpotIdDetector().

Referenced by LoadAlignChunk(), and LoadSeqChunk().

x_LoadRangesCov()

bool CBamRefSeqInfo::x_LoadRangesCov ( void  )

protected

Definition at line 1019 of file bamloader_impl.cpp.

References cnt, ctll::empty(), ERR_POST_X, eSerial_AsnBinary, g(), CAnnot_descr_Base::Get(), CSeq_graph_Base::GetA(), CBioseq_Base::GetAnnot(), CSeq_graph_Base::GetB(), CBamFileInfo::GetBamDb(), CSeq_graph_Base::C_Graph::GetByte(), CSeq_graph_Base::GetComp(), CUser_field_Base::GetData(), CSeq_annot_Base::GetData(), GetDebugLevel(), CSeq_annot_Base::GetDesc(), CUser_object::GetField(), CUser_object::GetFieldRef(), CSeq_annot_Base::C_Data::GetGraph(), CSeq_graph_Base::GetGraph(), GetIdField(), CUser_field_Base::C_Data::GetInt(), CSeq_graph_Base::C_Graph::GetInt(), CSeq_graph_Base::GetNumval(), GetPreferRawIndexOverCoverageGraphParam(), CUser_field_Base::C_Data::GetReal(), CSeq_entry_Base::GetSeq(), i, in(), Info(), int, CSeq_graph_Base::C_Graph::IsByte(), ITERATE, kChunkSize, kInvalidSeqPos, LOG_POST_X, CBamRefSeqChunkInfo::m_AlignCount, m_Chunks, m_CovEntry, m_CovFileName, m_File, CBamRefSeqChunkInfo::m_MaxRefSeqFrom, m_MinMapQuality, CBamRefSeqChunkInfo::m_RefSeqRange, max(), NCBI_THROW_FMT, CObjectIStream::Open(), CRange_Base::SetFrom(), COpenRange< Position >::SetToOpen(), and CBamDb::UsesRawIndex().

Referenced by LoadRanges().

x_LoadRangesEstimated()

bool CBamRefSeqInfo::x_LoadRangesEstimated ( void  )

protected

Definition at line 1181 of file bamloader_impl.cpp.

References _ASSERT, SBamIndexRefIndex::EstimateDataSizeByAlnStartPos(), CBamFileInfo::GetAnnotName(), CBamFileInfo::GetBamDb(), CBamFileInfo::GetBamName(), GetDebugLevel(), GetEstimatedCoverageGraphParam(), CBamRawDb::GetIndex(), SBamIndexParams::GetMinBinSize(), GetPileupGraphsParam(), CBamDb::GetRawDb(), CBamIndex::GetRef(), CBamRawDb::GetRefIndex(), GetRefSeq_id(), GetRefSeqId(), CBamRawDb::GetRefSeqLength(), GetSeqId(), GetSplitBinDataSize(), GetSplitBinMinLength(), i, Info(), info, kChunkDataSize, kInvalidSeqPos, kMax_UI8, LOG_POST_X, m_Chunks, m_CovEntry, m_File, m_MinMapQuality, CBam2Seq_graph::MakeSeq_annot(), s_GetEnd(), CSeq_entry::SetAnnot(), CBam2Seq_graph::SetAnnotName(), CBam2Seq_graph::SetEstimated(), CBam2Seq_graph::SetMinMapQuality(), CBam2Seq_graph::SetRefId(), CBam2Seq_graph::SetRefLabel(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CBamDb::UsesRawIndex().

Referenced by LoadRanges().

x_LoadRangesScan()

void CBamRefSeqInfo::x_LoadRangesScan ( void  )

protected

Definition at line 1458 of file bamloader_impl.cpp.

References _TRACE, CBamRefSeqChunkInfo::AddRefSeqRange(), GetDebugLevel(), GetRefSeqId(), CBamFileInfo::GetRefSeqLength(), i, Info(), kChunkSize, LOG_POST_X, m_Chunks, m_File, m_MinMapQuality, max(), min(), and ct::sort().

x_LoadRangesStat()

void CBamRefSeqInfo::x_LoadRangesStat ( void  )

protected

Definition at line 1362 of file bamloader_impl.cpp.

References _TRACE, GetDebugLevel(), GetRefSeqId(), CBamFileInfo::GetRefSeqLength(), Info(), kChunkSize, kInvalidSeqPos, kNumStat, LOG_POST_X, CBamRefSeqChunkInfo::m_AlignCount, m_Chunks, m_File, m_LoadedRanges, CBamRefSeqChunkInfo::m_MaxRefSeqFrom, m_MinMapQuality, CBamRefSeqChunkInfo::m_RefSeqRange, max(), min(), CRange_Base::SetFrom(), and COpenRange< Position >::SetToOpen().

Referenced by LoadRanges().

Member Data Documentation

m_Chunks

TChunks CBamRefSeqInfo::m_Chunks

protected

Definition at line 200 of file bamloader_impl.hpp.

Referenced by CreateChunks(), GetChunkGraphRange(), LoadAlignChunk(), LoadPileupChunk(), LoadSeqChunk(), x_AddSeqChunk(), x_InitAlignIterator(), x_LoadRangesCov(), x_LoadRangesEstimated(), x_LoadRangesScan(), and x_LoadRangesStat().

m_CovEntry

CRef<CSeq_entry> CBamRefSeqInfo::m_CovEntry

protected

Definition at line 198 of file bamloader_impl.hpp.

Referenced by LoadMainChunk(), LoadMainEntry(), LoadMainSplit(), x_LoadRangesCov(), and x_LoadRangesEstimated().

m_CovFileName

string CBamRefSeqInfo::m_CovFileName

protected

Definition at line 197 of file bamloader_impl.hpp.

Referenced by LoadMainSplit(), SetCovFileName(), and x_LoadRangesCov().

m_File

CBamFileInfo* CBamRefSeqInfo::m_File

protected

Definition at line 194 of file bamloader_impl.hpp.

Referenced by CreateChunks(), EstimateAlignLoadSeconds(), EstimatePileupLoadSeconds(), EstimateSeqLoadSeconds(), LoadAlignChunk(), LoadMainSplit(), LoadPileupChunk(), LoadSeqChunk(), SetBlobId(), x_AddSeqChunk(), x_InitAlignIterator(), x_LoadRangesCov(), x_LoadRangesEstimated(), x_LoadRangesScan(), and x_LoadRangesStat().

m_LoadedRanges

bool CBamRefSeqInfo::m_LoadedRanges

protected

Definition at line 201 of file bamloader_impl.hpp.

Referenced by LoadRanges(), and x_LoadRangesStat().

m_MinMapQuality

int CBamRefSeqInfo::m_MinMapQuality

protected

Definition at line 199 of file bamloader_impl.hpp.

Referenced by LoadAlignChunk(), LoadPileupChunk(), LoadSeqChunk(), x_LoadRangesCov(), x_LoadRangesEstimated(), x_LoadRangesScan(), and x_LoadRangesStat().

m_RefSeq_id

CSeq_id_Handle CBamRefSeqInfo::m_RefSeq_id

protected

Definition at line 196 of file bamloader_impl.hpp.

Referenced by GetRefSeq_id().

m_RefSeqId

string CBamRefSeqInfo::m_RefSeqId

protected

Definition at line 195 of file bamloader_impl.hpp.

Referenced by GetRefSeqId().

m_Seq2Chunk

TSeq2Chunk CBamRefSeqInfo::m_Seq2Chunk

protected

Definition at line 203 of file bamloader_impl.hpp.

Referenced by CreateChunks(), GetShortSeqBlobId(), LoadSeqChunk(), and x_AddSeqChunk().

m_Seq2ChunkMutex

CMutex CBamRefSeqInfo::m_Seq2ChunkMutex

mutableprotected

Definition at line 204 of file bamloader_impl.hpp.

Referenced by CreateChunks(), GetShortSeqBlobId(), LoadSeqChunk(), and x_AddSeqChunk().

m_SpotIdDetector

CIRef<CBamAlignIterator::ISpotIdDetector> CBamRefSeqInfo::m_SpotIdDetector

protected

Definition at line 202 of file bamloader_impl.hpp.

Referenced by CBamRefSeqInfo(), LoadPileupChunk(), LoadSeqChunk(), and x_InitAlignIterator().

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

• include/sra/data_loaders/bam/impl/bamloader_impl.hpp
• src/sra/data_loaders/bam/bamloader_impl.cpp