CVcfReader Class Reference

Search Toolkit Book for CVcfReader

#include <objtools/readers/vcf_reader.hpp>

Inheritance diagram for CVcfReader:

Collaboration diagram for CVcfReader:

Public Types
enum	{ fNormal = 0 , fUseSetFormat = 1<<8 }
Public Types inherited from CReaderBase
enum	EFlags {   fNormal = 0 , fNumericIdsAsLocal = 1<<0 , fAllIdsAsLocal = 1<<1 , fNextInLine = 1<<2 ,   fAsRaw = 1<<3 }
	Customization flags that are relevant to all CReaderBase derived readers. More...
enum	ObjectType { OT_UNKNOWN , OT_SEQANNOT , OT_SEQENTRY }
using	TReaderLine = struct SReaderLine { SReaderLine(unsigned int line, string data):mLine(line), mData(data) {}
using	TReaderData = vector< TReaderLine >
using	TReaderFlags = long
typedef list< CRef< CSeq_annot > >	TAnnotList
typedef TAnnotList	TAnnots
typedef TAnnots::iterator	TAnnotIt
typedef TAnnots::const_iterator	TAnnotCit
using	SeqIdResolver = CRef< CSeq_id >(*)(const string &, long, bool)

Public Member Functions
	CVcfReader (int=0, CReaderListener *=nullptr)
virtual	~CVcfReader ()
CRef< CSeq_annot >	ReadSeqAnnot (ILineReader &, ILineErrorListener *=nullptr) override
	Read an object from a given line reader, render it as a single Seq-annot, if possible. More...
Public Member Functions inherited from CReaderBase
virtual	~CReaderBase ()
virtual CRef< CSerialObject >	ReadObject (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)
	Read an object from a given input stream, render it as the most appropriate Genbank object. More...
virtual CRef< CSerialObject >	ReadObject (ILineReader &lr, ILineErrorListener *pErrors=nullptr)
	Read an object from a given line reader, render it as the most appropriate Genbank object. More...
virtual CRef< CSeq_annot >	ReadSeqAnnot (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)
	Read an object from a given input stream, render it as a single Seq-annot. More...
virtual void	ReadSeqAnnots (TAnnots &annots, CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)
	Read all objects from given insput stream, returning them as a vector of Seq-annots. More...
virtual void	ReadSeqAnnots (TAnnots &annots, ILineReader &lr, ILineErrorListener *pErrors=nullptr)
	Read all objects from given insput stream, returning them as a vector of Seq-annots. More...
virtual CRef< CSeq_entry >	ReadSeqEntry (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)
	Read an object from a given input stream, render it as a single Seq-entry, if possible. More...
virtual CRef< CSeq_entry >	ReadSeqEntry (ILineReader &lr, ILineErrorListener *pErrors=nullptr)
	Read an object from a given line reader, render it as a single Seq-entry, if possible. More...
void	SetProgressReportInterval (unsigned int intv)
void	SetCanceler (ICanceled *=nullptr)
bool	IsCanceled () const

Protected Member Functions
CRef< CSeq_annot >	xCreateSeqAnnot () override
void	xGetData (ILineReader &, TReaderData &) override
void	xProcessData (const TReaderData &, CSeq_annot &) override
bool	xIsCommentLine (const CTempString &) override
virtual bool	xProcessTrackLine (const string &, CSeq_annot &)
virtual bool	xProcessMetaLine (const string &, CSeq_annot &)
virtual void	xSetFileFormat (const string &, CSeq_annot &, bool &)
virtual bool	xProcessMetaLineInfo (const string &, CSeq_annot &)
virtual bool	xProcessMetaLineFilter (const string &, CSeq_annot &)
virtual bool	xProcessMetaLineFormat (const string &, CSeq_annot &)
virtual bool	xProcessHeaderLine (const string &, CSeq_annot &)
virtual bool	xProcessDataLine (const string &, CSeq_annot &)
virtual bool	xAssignVcfMeta (CSeq_annot &)
virtual bool	xAssignVariationAlleleSet (const CVcfData &, CRef< CSeq_feat >)
virtual bool	xAssignFeatureLocationSet (const CVcfData &, CRef< CSeq_feat >)
virtual bool	xAssignVariationIds (CVcfData &, CRef< CSeq_feat >)
virtual bool	xAssignVariantSnv (const CVcfData &, unsigned int, CRef< CSeq_feat >)
virtual bool	xAssignVariantMnv (const CVcfData &, unsigned int, CRef< CSeq_feat >)
virtual bool	xAssignVariantDel (const CVcfData &, unsigned int, CRef< CSeq_feat >)
virtual bool	xAssignVariantIns (const CVcfData &, unsigned int, CRef< CSeq_feat >)
virtual bool	xAssignVariantDelins (const CVcfData &, unsigned int, CRef< CSeq_feat >)
virtual bool	xAssignVariantProps (CVcfData &, CRef< CSeq_feat >)
void	xAssignVariantSource (CVcfData &, CRef< CSeq_feat >)
virtual bool	xProcessScore (CVcfData &, CRef< CSeq_feat >)
virtual bool	xProcessFilter (CVcfData &, CRef< CSeq_feat >)
virtual bool	xProcessInfo (CVcfData &, CRef< CSeq_feat >)
virtual bool	xProcessFormat (CVcfData &, CRef< CSeq_feat >)
virtual bool	xParseData (const string &, CVcfData &, ILineErrorListener *=nullptr)
virtual bool	xNormalizeData (CVcfData &, ILineErrorListener *=nullptr)
Protected Member Functions inherited from CReaderBase
	CReaderBase (TReaderFlags flags=0, const string &name="", const string &title="", SeqIdResolver seqresolver=CReadUtil::AsSeqId, CReaderListener *pListener=nullptr)
	Protected constructor. Use GetReader() to get an actual reader object. More...
	CReaderBase (const CReaderBase &)=delete
	CReaderBase (CReaderBase &&)=delete
void	xGuardedGetData (ILineReader &, TReaderData &, ILineErrorListener *)
virtual void	xGuardedProcessData (const TReaderData &, CSeq_annot &, ILineErrorListener *)
virtual void	xValidateAnnot (const CSeq_annot &)
virtual bool	xGetLine (ILineReader &, string &)
virtual bool	xUngetLine (ILineReader &)
virtual bool	xIsTrackLine (const CTempString &)
virtual bool	xIsBrowserLine (const CTempString &)
virtual bool	xIsTrackTerminator (const CTempString &)
virtual void	xAssignTrackData (CSeq_annot &)
virtual bool	xParseBrowserLine (const string &, CSeq_annot &)
virtual bool	xParseTrackLine (const string &)
virtual void	xSetBrowserRegion (const string &, CAnnot_descr &)
virtual void	xPostProcessAnnot (CSeq_annot &)
virtual void	xAddConversionInfo (CSeq_annot &, ILineErrorListener *)
bool	xParseComment (const CTempString &, CRef< CSeq_annot > &)
virtual bool	xReadInit ()
virtual bool	xProgressInit (ILineReader &istr)
bool	xIsReportingProgress () const
bool	xIsOperationCanceled () const
void	xReportProgress (ILineErrorListener *=nullptr)
void	ProcessError (CObjReaderLineException &, ILineErrorListener *)
void	ProcessError (CLineError &, ILineErrorListener *)
void	ProcessWarning (CObjReaderLineException &, ILineErrorListener *)
void	ProcessWarning (CLineError &, ILineErrorListener *)
void	xProcessReaderMessage (CReaderMessage &, ILineErrorListener *)
void	xProcessLineError (const ILineError &, ILineErrorListener *)
void	xProcessUnknownException (const CException &)

Protected Attributes
double	mActualVersion
CRef< CAnnotdesc >	m_Meta
map< string, CVcfInfoSpec >	m_InfoSpecs
map< string, CVcfFormatSpec >	m_FormatSpecs
map< string, CVcfFilterSpec >	m_FilterSpecs
vector< string >	m_MetaDirectives
vector< string >	m_GenotypeHeaders
CMessageListenerLenient	m_ErrorsPrivate
bool	m_MetaHandled
Protected Attributes inherited from CReaderBase
unsigned int	m_uLineNumber
unsigned int	m_uDataCount = 0
unsigned int	m_uProgressReportInterval
unsigned int	m_uNextProgressReport
TReaderFlags	m_iFlags
string	m_AnnotName
string	m_AnnotTitle
string	m_PendingLine
unique_ptr< CTrackData >	m_pTrackDefaults
ILineReader *	m_pReader
ICanceled *	m_pCanceler
SeqIdResolver	mSeqIdResolve
unique_ptr< CReaderMessageHandler >	m_pMessageHandler

Static Protected Attributes
static const double	mMaxSupportedVersion = 4.1

Private Member Functions
bool	xAssigndbSNPTag (const vector< string > &ids, CRef< CDbtag > pDbtag) const

Additional Inherited Members
Static Public Member Functions inherited from CReaderBase
static CReaderBase *	GetReader (CFormatGuess::EFormat format, TReaderFlags flags=0, CReaderListener *=nullptr)
	Allocate a CReaderBase derived reader object based on the given file format. More...
Public Attributes inherited from CReaderBase
unsigned int	mLine
string	mData
Static Protected Member Functions inherited from CReaderBase
static void	xAddStringFlagsWithMap (const list< string > &stringFlags, const map< string, TReaderFlags > flagMap, TReaderFlags &baseFlags)

Detailed Description

Definition at line 142 of file vcf_reader.hpp.

Member Enumeration Documentation

anonymous enum

anonymous enum

Enumerator
fNormal
fUseSetFormat

Definition at line 150 of file vcf_reader.hpp.

Constructor & Destructor Documentation

CVcfReader()

CVcfReader::CVcfReader	(	int	flags = 0,
		CReaderListener *	pRL = nullptr
	)

Definition at line 162 of file vcf_reader.cpp.

~CVcfReader()

CVcfReader::~CVcfReader ( )

virtual

Definition at line 174 of file vcf_reader.cpp.

Member Function Documentation

ReadSeqAnnot()

CRef< CSeq_annot > CVcfReader::ReadSeqAnnot ( ILineReader &  lr, ILineErrorListener *  pErrors = nullptr  )

overridevirtual

Read an object from a given line reader, render it as a single Seq-annot, if possible.

Return empty Seq-annot otherwise.

Parameters

lr	line reader to read from.
pErrors	pointer to optional error container object.

Reimplemented from CReaderBase.

Definition at line 181 of file vcf_reader.cpp.

References lr(), m_Meta, CReaderBase::ReadSeqAnnot(), CRef< C, Locker >::Reset(), CUser_object_Base::SetType(), CAnnotdesc_Base::SetUser(), CReaderBase::xAssignTrackData(), and xAssignVcfMeta().

Referenced by CVcfObjectLoader::Execute().

xAssigndbSNPTag()

bool CVcfReader::xAssigndbSNPTag ( const vector< string > &  ids, CRef< CDbtag >  pDbtag  ) const

private

Definition at line 1296 of file vcf_reader.cpp.

References NStr::StartsWith(), and NStr::StringToInt().

Referenced by xAssignVariantSource(), and xAssignVariationIds().

xAssignFeatureLocationSet()

bool CVcfReader::xAssignFeatureLocationSet ( const CVcfData &  data, CRef< CSeq_feat >  pFeat  )

protectedvirtual

Definition at line 1101 of file vcf_reader.cpp.

References CReadUtil::AsSeqId(), data, CReaderBase::m_iFlags, CSeq_feat_Base::SetLocation(), CVcfData::ST_ALL_DEL, CVcfData::ST_ALL_INS, CVcfData::ST_ALL_MNV, and CVcfData::ST_ALL_SNV.

Referenced by xProcessDataLine().

xAssignVariantDel()

bool CVcfReader::xAssignVariantDel ( const CVcfData &  data, unsigned int  index, CRef< CSeq_feat >  pFeature  )

protectedvirtual

Definition at line 796 of file vcf_reader.cpp.

References s_AddDeleteDeltaItem(), and CSeq_feat_Base::SetData().

Referenced by xAssignVariationAlleleSet().

xAssignVariantDelins()

bool CVcfReader::xAssignVariantDelins ( const CVcfData &  data, unsigned int  index, CRef< CSeq_feat >  pFeature  )

protectedvirtual

Definition at line 850 of file vcf_reader.cpp.

References data, CVariation_inst_Base::eType_delins, CVariation_inst_Base::eType_snv, s_AddDeleteDeltaItem(), CSeq_feat_Base::SetData(), CVariation_inst_Base::SetDelta(), CSeq_literal_Base::SetLength(), CSeq_literal_Base::SetSeq_data(), and CVariation_inst_Base::SetType().

Referenced by xAssignVariationAlleleSet().

xAssignVariantIns()

bool CVcfReader::xAssignVariantIns ( const CVcfData &  data, unsigned int  index, CRef< CSeq_feat >  pFeature  )

protectedvirtual

Definition at line 819 of file vcf_reader.cpp.

References data, CDelta_item_Base::eAction_ins_before, CVariation_inst_Base::eType_ins, CSeq_feat_Base::SetData(), CVariation_inst_Base::SetDelta(), CSeq_literal_Base::SetLength(), CSeq_literal_Base::SetSeq_data(), and CVariation_inst_Base::SetType().

Referenced by xAssignVariationAlleleSet().

xAssignVariantMnv()

bool CVcfReader::xAssignVariantMnv ( const CVcfData &  data, unsigned int  index, CRef< CSeq_feat >  pFeature  )

protectedvirtual

Definition at line 761 of file vcf_reader.cpp.

References data, CVariation_ref::eSeqType_na, and CSeq_feat_Base::SetData().

Referenced by xAssignVariationAlleleSet().

xAssignVariantProps()

bool CVcfReader::xAssignVariantProps ( CVcfData &  data, CRef< CSeq_feat >  pFeat  )

protectedvirtual

Definition at line 1385 of file vcf_reader.cpp.

References data, eDiag_Warning, CVariantProperties_Base::eGene_location_utr_3, map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), CReaderBase::m_pMessageHandler, CReaderBase::m_uLineNumber, CSeq_feat_Base::SetData(), CDbtag_Base::SetDb(), CSeq_feat_Base::SetDbxref(), CDbtag_Base::SetTag(), NStr::SplitInTwo(), NStr::StringToDouble(), NStr::StringToInt(), tag, weight, and xAssignVariantSource().

Referenced by xProcessInfo().

xAssignVariantSnv()

bool CVcfReader::xAssignVariantSnv ( const CVcfData &  data, unsigned int  index, CRef< CSeq_feat >  pFeature  )

protectedvirtual

Definition at line 740 of file vcf_reader.cpp.

References data, CVariation_ref::eSeqType_na, and CSeq_feat_Base::SetData().

Referenced by xAssignVariationAlleleSet().

xAssignVariantSource()

void CVcfReader::xAssignVariantSource ( CVcfData &  data, CRef< CSeq_feat >  pFeat  )

protected

Definition at line 1651 of file vcf_reader.cpp.

References data, eDiag_Warning, map_checker< Container >::end(), NStr::Equal(), map_checker< Container >::erase(), map_checker< Container >::find(), CReaderBase::m_pMessageHandler, CReaderBase::m_uLineNumber, CSeq_feat_Base::SetDbxref(), and xAssigndbSNPTag().

Referenced by xAssignVariantProps().

xAssignVariationAlleleSet()

bool CVcfReader::xAssignVariationAlleleSet ( const CVcfData &  data, CRef< CSeq_feat >  pFeature  )

protectedvirtual

Definition at line 662 of file vcf_reader.cpp.

References data, CVariation_inst_Base::eObservation_reference, CVariation_inst_Base::eObservation_variant, NStr::Equal(), CVariation_ref::eSeqType_na, CVariation_inst_Base::eType_identity, i, CSeq_feat_Base::SetData(), CVariation_inst_Base::SetObservation(), CVariation_inst_Base::SetType(), CVcfData::ST_ALL_DEL, CVcfData::ST_ALL_INS, CVcfData::ST_ALL_MNV, CVcfData::ST_ALL_SNV, xAssignVariantDel(), xAssignVariantDelins(), xAssignVariantIns(), xAssignVariantMnv(), and xAssignVariantSnv().

Referenced by xProcessDataLine().

xAssignVariationIds()

bool CVcfReader::xAssignVariationIds ( CVcfData &  data, CRef< CSeq_feat >  pFeature  )

protectedvirtual

Definition at line 1322 of file vcf_reader.cpp.

References data, NStr::Equal(), CRef< C, Locker >::GetNCObject(), i, Ref(), CSeq_feat_Base::SetData(), NStr::StartsWith(), NStr::ToLower(), and xAssigndbSNPTag().

Referenced by xProcessDataLine().

xAssignVcfMeta()

bool CVcfReader::xAssignVcfMeta ( CSeq_annot &  annot )

protectedvirtual

Definition at line 588 of file vcf_reader.cpp.

References CAnnotdesc_Base::GetUser(), CUser_object_Base::IsSetData(), CSeq_annot_Base::IsSetDesc(), CAnnotdesc_Base::IsUser(), m_Meta, and CSeq_annot_Base::SetDesc().

Referenced by ReadSeqAnnot().

xCreateSeqAnnot()

CRef< CSeq_annot > CVcfReader::xCreateSeqAnnot ( )

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 200 of file vcf_reader.cpp.

References CSeq_annot_Base::SetData(), and CReaderBase::xCreateSeqAnnot().

xGetData()

void CVcfReader::xGetData ( ILineReader &  lr, TReaderData &  readerData  )

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 210 of file vcf_reader.cpp.

References lr(), CReaderBase::m_uDataCount, CReaderBase::m_uLineNumber, CReaderBase::xGetLine(), CReaderBase::xIsTrackLine(), and CReaderBase::xUngetLine().

xIsCommentLine()

bool CVcfReader::xIsCommentLine ( const CTempString &  strLine )

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 1683 of file vcf_reader.cpp.

References NStr::StartsWith(), and CReaderBase::xIsCommentLine().

xNormalizeData()

bool CVcfReader::xNormalizeData ( CVcfData &  data, ILineErrorListener *  pEC = nullptr  )

protectedvirtual

Definition at line 1026 of file vcf_reader.cpp.

References CObjReaderLineException::Create(), data, eDiag_Error, ILineError::eProblem_GeneralParsingError, CReaderBase::ProcessError(), and NStr::StartsWith().

Referenced by xParseData().

xParseData()

bool CVcfReader::xParseData ( const string &  line, CVcfData &  data, ILineErrorListener *  pEC = nullptr  )

protectedvirtual

Definition at line 895 of file vcf_reader.cpp.

References columns, CObjReaderLineException::Create(), data, eDiag_Error, ILineError::eProblem_GeneralParsingError, NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, ncbi::grid::netcache::search::fields::key, m_GenotypeHeaders, CReaderBase::ProcessError(), NStr::Split(), NStr::SplitInTwo(), CVcfData::ST_ALL_DEL, CVcfData::ST_ALL_INS, CVcfData::ST_ALL_MNV, CVcfData::ST_ALL_SNV, CVcfData::ST_MIXED, NStr::StartsWith(), NStr::StringToDouble(), NStr::StringToInt(), rapidjson::value, and xNormalizeData().

Referenced by xProcessDataLine().

xProcessData()

void CVcfReader::xProcessData ( const TReaderData &  readerData, CSeq_annot &  annot  )

overrideprotectedvirtual

Reimplemented from CReaderBase.

Definition at line 229 of file vcf_reader.cpp.

References eDiag_Warning, CReaderBase::m_pMessageHandler, CReaderBase::m_uDataCount, CReaderBase::m_uLineNumber, mActualVersion, CReaderBase::xParseBrowserLine(), xProcessDataLine(), xProcessHeaderLine(), xProcessMetaLine(), xProcessTrackLine(), and xSetFileFormat().

xProcessDataLine()

bool CVcfReader::xProcessDataLine ( const string &  line, CSeq_annot &  annot  )

protectedvirtual

Definition at line 611 of file vcf_reader.cpp.

References data, CUser_object_Base::GetData(), CSeq_feat_Base::GetExt(), CSeq_feat_Base::ResetExt(), CSeq_annot_Base::SetData(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetExt(), CUser_object_Base::SetType(), NStr::StartsWith(), xAssignFeatureLocationSet(), xAssignVariationAlleleSet(), xAssignVariationIds(), xParseData(), xProcessFilter(), xProcessFormat(), xProcessInfo(), and xProcessScore().

Referenced by xProcessData().

xProcessFilter()

bool CVcfReader::xProcessFilter ( CVcfData &  data, CRef< CSeq_feat >  pFeature  )

protectedvirtual

Definition at line 1193 of file vcf_reader.cpp.

References CUser_object::AddField(), data, NStr::Equal(), and CSeq_feat_Base::SetExt().

Referenced by xProcessDataLine().

xProcessFormat()

bool CVcfReader::xProcessFormat ( CVcfData &  data, CRef< CSeq_feat >  pFeature  )

protectedvirtual

Definition at line 1271 of file vcf_reader.cpp.

References CUser_object::AddField(), CUser_field::AddField(), data, CUser_object_Base::SetData(), CSeq_feat_Base::SetExt(), and CUser_field_Base::SetLabel().

Referenced by xProcessDataLine().

xProcessHeaderLine()

bool CVcfReader::xProcessHeaderLine ( const string &  line, CSeq_annot &  annot  )

protectedvirtual

Definition at line 551 of file vcf_reader.cpp.

References CUser_object::AddField(), NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, m_GenotypeHeaders, m_Meta, CAnnotdesc_Base::SetUser(), NStr::Split(), and NStr::StartsWith().

Referenced by xProcessData().

xProcessInfo()

bool CVcfReader::xProcessInfo ( CVcfData &  data, CRef< CSeq_feat >  pFeature  )

protectedvirtual

Definition at line 1207 of file vcf_reader.cpp.

References CUser_object::AddField(), data, NStr::Join(), ncbi::grid::netcache::search::fields::key, CSeq_feat_Base::SetExt(), rapidjson::value, and xAssignVariantProps().

Referenced by xProcessDataLine().

xProcessMetaLine()

bool CVcfReader::xProcessMetaLine ( const string &  line, CSeq_annot &  annot  )

protectedvirtual

Definition at line 276 of file vcf_reader.cpp.

References CUser_object::AddField(), m_Meta, m_MetaDirectives, m_MetaHandled, CAnnotdesc_Base::SetUser(), NStr::StartsWith(), xProcessMetaLineFilter(), xProcessMetaLineFormat(), and xProcessMetaLineInfo().

Referenced by xProcessData().

xProcessMetaLineFilter()

bool CVcfReader::xProcessMetaLineFilter ( const string &  line, CSeq_annot &  annot  )

protectedvirtual

Definition at line 432 of file vcf_reader.cpp.

References CObjReaderLineException::Create(), eDiag_Error, NStr::EndsWith(), ILineError::eProblem_BadFilterLine, info, ncbi::grid::netcache::search::fields::key, m_FilterSpecs, CReaderBase::ProcessError(), NStr::Split(), NStr::SplitInTwo(), and NStr::StartsWith().

Referenced by xProcessMetaLine().

xProcessMetaLineFormat()

bool CVcfReader::xProcessMetaLineFormat ( const string &  line, CSeq_annot &  annot  )

protectedvirtual

Definition at line 480 of file vcf_reader.cpp.

References CObjReaderLineException::Create(), eDiag_Error, NStr::EndsWith(), ILineError::eProblem_BadFormatLine, info, ncbi::grid::netcache::search::fields::key, m_FormatSpecs, CReaderBase::ProcessError(), NStr::Split(), NStr::SplitInTwo(), NStr::StartsWith(), and type.

Referenced by xProcessMetaLine().

xProcessMetaLineInfo()

bool CVcfReader::xProcessMetaLineInfo ( const string &  line, CSeq_annot &  annot  )

protectedvirtual

Definition at line 364 of file vcf_reader.cpp.

References CObjReaderLineException::Create(), eDiag_Error, NStr::EndsWith(), ILineError::eProblem_BadInfoLine, info, ncbi::grid::netcache::search::fields::key, m_InfoSpecs, CReaderBase::ProcessError(), NStr::Split(), NStr::SplitInTwo(), NStr::StartsWith(), and type.

Referenced by xProcessMetaLine().

xProcessScore()

bool CVcfReader::xProcessScore ( CVcfData &  data, CRef< CSeq_feat >  pFeature  )

protectedvirtual

Definition at line 1179 of file vcf_reader.cpp.

References CUser_object::AddField(), data, and CSeq_feat_Base::SetExt().

Referenced by xProcessDataLine().

xProcessTrackLine()

bool CVcfReader::xProcessTrackLine ( const string &  strLine, CSeq_annot &  current  )

protectedvirtual

Definition at line 1239 of file vcf_reader.cpp.

References eDiag_Warning, CReaderBase::m_pMessageHandler, CReaderBase::m_uLineNumber, CReadUtil::Tokenize(), CReaderBase::xIsTrackLine(), and CReaderBase::xParseTrackLine().

Referenced by xProcessData().

xSetFileFormat()

void CVcfReader::xSetFileFormat ( const string &  line, CSeq_annot &  annot, bool &  lineContainsVersion  )

protectedvirtual

Definition at line 304 of file vcf_reader.cpp.

References NStr::DoubleToString(), eDiag_Warning, CReaderBase::m_pMessageHandler, CReaderBase::m_uLineNumber, mActualVersion, mMaxSupportedVersion, NStr::StartsWith(), and NStr::StringToDouble().

Referenced by xProcessData().

Member Data Documentation

m_ErrorsPrivate

CMessageListenerLenient CVcfReader::m_ErrorsPrivate

protected

Definition at line 335 of file vcf_reader.hpp.

m_FilterSpecs

map<string,CVcfFilterSpec> CVcfReader::m_FilterSpecs

protected

Definition at line 332 of file vcf_reader.hpp.

Referenced by xProcessMetaLineFilter().

m_FormatSpecs

map<string,CVcfFormatSpec> CVcfReader::m_FormatSpecs

protected

Definition at line 331 of file vcf_reader.hpp.

Referenced by xProcessMetaLineFormat().

m_GenotypeHeaders

vector<string> CVcfReader::m_GenotypeHeaders

protected

Definition at line 334 of file vcf_reader.hpp.

Referenced by xParseData(), and xProcessHeaderLine().

m_InfoSpecs

map<string,CVcfInfoSpec> CVcfReader::m_InfoSpecs

protected

Definition at line 330 of file vcf_reader.hpp.

Referenced by xProcessMetaLineInfo().

m_Meta

CRef< CAnnotdesc > CVcfReader::m_Meta

protected

Definition at line 329 of file vcf_reader.hpp.

Referenced by ReadSeqAnnot(), xAssignVcfMeta(), xProcessHeaderLine(), and xProcessMetaLine().

m_MetaDirectives

vector<string> CVcfReader::m_MetaDirectives

protected

Definition at line 333 of file vcf_reader.hpp.

Referenced by xProcessMetaLine().

m_MetaHandled

bool CVcfReader::m_MetaHandled

protected

Definition at line 336 of file vcf_reader.hpp.

Referenced by xProcessMetaLine().

mActualVersion

double CVcfReader::mActualVersion

protected

Definition at line 328 of file vcf_reader.hpp.

Referenced by xProcessData(), and xSetFileFormat().

mMaxSupportedVersion

const double CVcfReader::mMaxSupportedVersion = 4.1

staticprotected

Definition at line 327 of file vcf_reader.hpp.

Referenced by xSetFileFormat().

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

• include/objtools/readers/vcf_reader.hpp
• src/objtools/readers/vcf_reader.cpp