Search Toolkit Book for CVCFVariantList

#include <gui/widgets/loaders/columnar_vcf_variants.hpp>

Inheritance diagram for CVCFVariantList:

Collaboration diagram for CVCFVariantList:

Public Member Functions
	CVCFVariantList (const string &chr_name, bool load_all_info=true, const set< string > &info_fields=set< string >(), const map< unsigned, string > &sample_cols=map< unsigned, string >())

	CVCFVariantList (const string &chr_name, const vector< char > &data)

	CVCFVariantList (const string &chr_name, const string &filename)

	CVCFVariantList (const vector< char > &data, const string &data_version)

	~CVCFVariantList ()

void	ParseLine (const string &line)

void	FinalizeReading ()

virtual bool	GetPositionsForVariant (const string &variant_id, vector< unsigned > &positions)

virtual void	GetPositionsForMissingVarID (vector< unsigned > &positions)

const string &	GetChrName () const

const vector< char > &	GetSerializedData () const

void	WriteSerializedData (const string &filename)

bool	AreVariantIdsUnique (vector< pair< string, unsigned >> &copies)

void	List (CNcbiOstream &out, bool only_sv_cols=false) const

void	ListSamples (CNcbiOstream &out) const

vector< string >	GetAllVariantIDS () const

bool	operator== (const CVCFVariantList &other) const

	CVCFVariantList (const CVCFVariantList &)=delete

CVCFVariantList &	operator= (const CVCFVariantList &)=delete

bool	SerializeVariantData (const string &prefix, CNcbiOstream *out=nullptr)

bool	DeserializeAndCheck (const string &prefix, CNcbiOstream *out=nullptr)

bool	RemoveSerializedOutput (const string &prefix)

void	GetStatistics (CNcbiOstream &out)

Public Member Functions inherited from CVCFVariantsBase
virtual	~CVCFVariantsBase ()

const CVariantDescriptors &	GetDescriptors () const

unsigned	GetPositionForIndex (const size_t &index) const

size_t	GetIndexForPosition (const unsigned &pos, CPosToIndex::EType type) const

TSeqPos	GetStart () const

TSeqPos	GetStop () const

unsigned	Count () const

unsigned	Count (const TSeqRange &range) const

void	GetHistogram (svector &hist, const svector::size_type &bin_width) const

void	GetHistogram (TIndexVector &hist, const svector::size_type &bin_width)

bool	operator== (const CVCFVariantsBase &other) const

void	ListPositionVectors (CNcbiOstream &out) const

TSeqPos	GetLeftShiftedStartPos (const TSeqRange &range) const

const vector< size_t > *	GetIncludedItems () const

unique_ptr< vector< size_t > >	Filter (const TSeqRange &range) const

	CVCFVariantsBase (const CVCFVariantsBase &)=delete

CVCFVariantsBase &	operator= (const CVCFVariantsBase &)=delete

size_t	GetNumberOfIndexVecs () const

const size_t &	GetMaxIndex () const

const unsigned &	GetMaxFeatLength () 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

Private Member Functions
string	x_ParseNextColumn (string &line, size_t &pos)

string	x_GetFilePrefix (const string &prefix) const

Private Attributes
string	m_ChrName

size_t	m_Index { 0 }

Additional Inherited Members
Public Types inherited from CVCFVariantsBase
using	TSparseStrVector = CVariantDescriptors::TSparseStrVector

using	TSparseOptVector = CVariantDescriptors::TSparseOptVector

using	TIndexVector = CPosToIndex::TIndexVector

using	svector = CPosToIndex::svector

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 CVCFVariantsBase
static const vector< string > &	s_GetColNames ()
	does not contain sm_INFO and sm_SAMPLES More...

static const vector< string > &	s_GetAllColNames ()
	contains sm_INFO, sm_SAMPLES More...

static string	s_GetPreviousVersion ()

static string	s_GetCurrentVersion (bool format_only=false)

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 CVCFVariantsBase
static const string	sm_MissingValue = "."

static const string	sm_ID = "ID"

static const string	sm_REF = "REF"

static const string	sm_ALT = "ALT"

static const string	sm_QUAL = "QUAL"

static const string	sm_FILTER = "FILTER"

static const string	sm_INFO = "INFO"

static const string	sm_FORMAT = "FORMAT"

static const string	sm_SAMPLES = "SAMPLES"

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...

Protected Member Functions inherited from CVCFVariantsBase
	CVCFVariantsBase ()

	CVCFVariantsBase (bool load_info, const set< string > &info_fields, const map< unsigned, string > &sample_cols)

void	x_SerializeData () const

void	x_DeserializeAllData ()

void	x_DeserializeIndexVectors (const unsigned char *&buf_ptr, size_t &nr_cols, bool skip_feat_length=false)

void	x_DeserializeDescr_All (const unsigned char *buf_ptr, const size_t &nr_cols)

void	x_DeserializeDescr_Range (const unsigned char buf_ptr, const size_t &nr_cols, const TSeqRange range=nullptr, const set< string > &cols_to_decode=set< string >(), bool only_start=false)

bool	x_DeserializeColumn (const string &col_name, const unsigned char *buf_ptr, const size_t &nr_cols)

unique_ptr< vector< size_t > >	x_Filter (const TSeqPos &pos) const
	Returns a vector of indices of the variants that cross sequence position 'pos'. More...

unique_ptr< vector< size_t > >	x_NullOrFilterClinVar (const TSeqPos &pos) const

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes inherited from CVCFVariantsBase
CVariantDescriptors	m_Descriptors

CPosToIndex	m_Posindexmap

TSeqPos	m_StartPos { 0 }
	in genomic coordinates (1-based) More...

TSeqPos	m_StopPos { 0 }
	in genomic coordinates (1-based) More...

unsigned	m_MaxFeatLength { 0 }
	maximum feature variant length More...

unique_ptr< vector< size_t > >	m_VarsWithinRange
	variants included within a specific range More...

vector< char > *	m_Buffer { nullptr }

bm::sparse_vector_deserializer< TSparseStrVector >	m_Deserializer

bm::sparse_vector_deserializer< TSparseOptVector >	m_OptDeserializer

Detailed Description

Definition at line 50 of file columnar_vcf_variants.hpp.

Constructor & Destructor Documentation

◆ CVCFVariantList() [1/5]

CVCFVariantList::CVCFVariantList	(	const string &	chr_name,
		bool	load_all_info = `true`,
		const set< string > &	info_fields = `set<string>()`,
		const map< unsigned, string > &	sample_cols = `map<unsigned, string>()`
	)