#include <objtools/writers/vcf_writer.hpp>

Inheritance diagram for CVcfWriter:

Collaboration diagram for CVcfWriter:

Public Types
enum	TFlags { fNormal = 0 }

Public Types inherited from CWriterBase
enum	TFlags { fNormal = 0 , fDebugOutput = (1<<0) , fWriterBaseLast = fDebugOutput }
	Customization flags that are relevant to all CWriterBase derived writers. More...

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...

Public Member Functions
	CVcfWriter (CScope &, CNcbiOstream &, TFlags=fNormal)

virtual	~CVcfWriter ()

bool	WriteAnnot (const CSeq_annot &, const string &="", const string &="") override
	Write a raw Seq-annot to the internal output stream. More...

virtual SAnnotSelector &	SetAnnotSelector (void) override

Public Member Functions inherited from CWriterBase
virtual	~CWriterBase ()

virtual bool	WriteAlign (const CSeq_align &, const string &="", const string &="")
	Write a raw Seq-align to the internal output stream. More...

virtual bool	WriteSeqEntryHandle (CSeq_entry_Handle, const string &="", const string &="")
	Write a Seq-entry handle to the internal output stream. More...

virtual bool	WriteBioseqHandle (CBioseq_Handle, const string &="", const string &="")
	Write a Bioseq handle to the internal output stream. More...

virtual bool	WriteSeqAnnotHandle (CSeq_annot_Handle, const string &="", const string &="")
	Write a Seq-annot handle to the internal output stream. More...

virtual bool	WriteHeader ()
	Write a file header. More...

virtual bool	WriteHeader (const CSeq_annot &)
	Write a file header, using annotation information. More...

virtual bool	WriteFooter ()
	Write a file trailer. More...

void	SetMessageListener (CWriterListener *pMessageListener)

virtual void	PutMessage (const CWriterMessage &message)

SAnnotSelector &	GetAnnotSelector (void)

virtual CRange< TSeqPos > &	SetRange (void)

virtual const CRange< TSeqPos > &	GetRange (void) 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

Public Member Functions inherited from CInterruptable
	CInterruptable ()

virtual	~CInterruptable ()

void	SetCanceler (ICanceled *pCanceller)

bool	IsCanceled () const

Public Member Functions inherited from ICanceled
virtual	~ICanceled ()

Public Member Functions inherited from CFeatWriter
virtual	~CFeatWriter (void)=default

bool	WriteFeatures (CFeat_CI &first)

Protected Member Functions
void	x_GetTypeRefAlt (const CVariation_inst &inst, int &rtype, string &ref, list< int > &alt_types, vector< string > &alt)

bool	x_WriteInit (const CSeq_annot &)

bool	x_WriteMeta (const CSeq_annot &)

bool	x_WriteHeader (const CSeq_annot &)

bool	x_WriteData (const CSeq_annot &)

bool	x_WriteMetaCreateNew (const CSeq_annot &)

bool	xWriteFeature (CFeat_CI feat_it) override

bool	x_WriteFeature (const CMappedFeat &)

bool	x_WriteFeatureChrom (const CMappedFeat &)

bool	x_WriteFeaturePos (const CMappedFeat &, unsigned int start, const int type)

bool	x_WriteFeatureId (const CMappedFeat &)

bool	x_WriteFeatureRef (const unsigned int start, const int type, const string &anchor, const string &ref)

bool	x_WriteFeatureAlt (const unsigned int start, const int type, const string &anchor, const list< int > &alt_types, const vector< string > &alt)

bool	x_WriteFeatureQual (const CMappedFeat &)

bool	x_WriteFeatureFilter (const CMappedFeat &)

bool	x_WriteFeatureInfo (const CMappedFeat &)

bool	x_WriteFeatureGenotypeData (const CMappedFeat &)

Protected Member Functions inherited from CWriterBase
	CWriterBase (CNcbiOstream &ostr, unsigned int uFlags=0)

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

Protected Attributes
CScope &	m_Scope

vector< string >	m_GenotypeHeaders

Protected Attributes inherited from CWriterBase
CNcbiOstream &	m_Os

unsigned int	m_uFlags

unique_ptr< SAnnotSelector >	m_Selector

CRange< TSeqPos >	m_Range

CWriterListener *	mpMessageListener

Protected Attributes inherited from CInterruptable
ICanceled *	mpCancelled

Additional Inherited Members
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 43 of file vcf_writer.hpp.

Member Enumeration Documentation

◆ TFlags

enum CVcfWriter::TFlags

Enumerator
fNormal

Definition at line 48 of file vcf_writer.hpp.

Constructor & Destructor Documentation

◆ CVcfWriter()

CVcfWriter::CVcfWriter	(	CScope &	scope,
		CNcbiOstream &	ostr,
		TFlags	uFlags = `fNormal`
	)

Definition at line 100 of file vcf_writer.cpp.

◆ ~CVcfWriter()

CVcfWriter::~CVcfWriter ( )

virtual

Definition at line 111 of file vcf_writer.cpp.

Member Function Documentation

◆ SetAnnotSelector()

SAnnotSelector & CVcfWriter::SetAnnotSelector ( void )

overridevirtual

Reimplemented from CWriterBase.

Definition at line 166 of file vcf_writer.cpp.

References SAnnotSelector::eSortOrder_None, CWriterBase::m_Selector, CWriterBase::SetAnnotSelector(), and SAnnotSelector::SetSortOrder().

Referenced by WriteAnnot(), and x_WriteData().

◆ WriteAnnot()

bool CVcfWriter::WriteAnnot	(	const CSeq_annot &	,
		const string &	= `""`,
		const string &	= `""`
	)

overridevirtual

Write a raw Seq-annot to the internal output stream.

This implementation will just generate an error and then exit. It should be re-implemented in format specific subclasses.

Parameters

annot	the Seq-annot object to be written.
name	parameter describing the object. Handling will be format specific
descr	parameter describing the object. Handling will be format specific

Reimplemented from CWriterBase.

Definition at line 117 of file vcf_writer.cpp.

References CScope::AddSeq_annot(), CSerialObject::Assign(), ERR_POST, Error(), CVariationNormalization::eVCF, CScope::GetBioseqHandle(), CSeq_id::GetLabel(), CMappedFeat::GetLocation(), label, m_Scope, CVariationNormalization::NormalizeVariation(), SetAnnotSelector(), x_WriteData(), x_WriteHeader(), x_WriteInit(), and x_WriteMeta().

Referenced by sRunTest(), and sUpdateCase().

◆ x_GetTypeRefAlt()

void CVcfWriter::x_GetTypeRefAlt	(	const CVariation_inst &	inst,
		int &	rtype,
		string &	ref,
		list< int > &	alt_types,
		vector< string > &	alt
	)

protected

Definition at line 313 of file vcf_writer.cpp.

References a, CVariation_inst_Base::eType_del, CVariation_inst_Base::eType_delins, CVariation_inst_Base::eType_identity, CVariation_inst_Base::GetDelta(), CVariation_inst_Base::GetType(), and CVariation_inst_Base::IsSetDelta().

Referenced by x_WriteFeature().

◆ x_WriteData()

bool CVcfWriter::x_WriteData ( const CSeq_annot & annot )

protected

Definition at line 275 of file vcf_writer.cpp.

References SAnnotSelector::eSortOrder_None, CSeq_feat_Handle::GetOriginalSeq_feat(), CWriterBase::GetRange(), CScope::GetSeq_annotHandle(), CMappedFeat::GetSeq_feat_Handle(), CMappedFeat::GetTotalRange(), COpenRange< Position >::IntersectionWith(), m_Scope, COpenRange< Position >::NotEmpty(), compile_time_bits::range(), CSeq_feat_EditHandle::Replace(), SetAnnotSelector(), SAnnotSelector::SetSortOrder(), and x_WriteFeature().

Referenced by WriteAnnot().

◆ x_WriteFeature()

bool CVcfWriter::x_WriteFeature ( const CMappedFeat & mf )

protected

Definition at line 360 of file vcf_writer.cpp.

References CVariation_ref_Base::C_Data::e_Instance, CVariation_ref_Base::C_Data::e_Set, CBioseq_Handle::eCoding_Iupac, eExtreme_Positional, eNa_strand_unknown, ERR_POST, Error(), CVariation_inst_Base::eType_del, CVariation_inst_Base::eType_delins, CVariation_inst_Base::eType_identity, CVariation_inst_Base::eType_ins, CVariation_inst_Base::eType_mnp, CVariation_inst_Base::eType_snv, CScope::GetBioseqHandle(), CVariation_ref_Base::GetData(), CSeq_feat_Handle::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CSeq_id::GetLabel(), CMappedFeat::GetLocation(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CVariation_ref_Base::C_Data::GetSet(), CSeqFeatData_Base::GetVariation(), CVariation_ref_Base::C_Data::C_Set::GetVariations(), CInterruptable::IsCanceled(), label, CWriterBase::m_Os, m_Scope, msg(), NCBI_THROW, Warning(), CVariation_ref_Base::C_Data::Which(), x_GetTypeRefAlt(), x_WriteFeatureAlt(), x_WriteFeatureChrom(), x_WriteFeatureFilter(), x_WriteFeatureGenotypeData(), x_WriteFeatureId(), x_WriteFeatureInfo(), x_WriteFeaturePos(), x_WriteFeatureQual(), and x_WriteFeatureRef().

Referenced by x_WriteData(), and xWriteFeature().

◆ x_WriteFeatureAlt()

bool CVcfWriter::x_WriteFeatureAlt	(	const unsigned int	start,
		const int	type,
		const string &	anchor,
		const list< int > &	alt_types,
		const vector< string > &	alt
	)