NSNPVariationHelper Class Reference

Search Toolkit Book for NSNPVariationHelper

set of functions for dealing with SNP represented as variation objects More...

#include <objtools/snputil/snp_utils.hpp>

Public Types
enum	ESNPPropTypes {   eSNPPropName_Undef , eSNPPropName_GeneLocation , eSNPPropName_Effect , eSNPPropName_Mapping ,   eSNPPropName_FreqValidation , eSNPPropName_QualityCheck , eSNPPropName_ResourceLink , eSNPPropName_ResourceLinkURL }
	enums to control getting a string list representation of various CVariantProperties More...

Static Public Member Functions
static bool	ConvertFeat (CVariation &Variation, const CSeq_feat &SrcFeat)
	legacy SNP feature conversion into a variation object More...
static bool	ConvertFeat (CVariation_ref &Variation, const CSeq_feat &SrcFeat)
static void	DecodeBitfield (CVariantProperties &prop, const CSnpBitfield &bf)
	convert SNP bitfield data to respective fields in CVariantProperties More...
static void	VariantPropAsStrings (list< string > &ResList, const CVariantProperties &prop, ESNPPropTypes ePropType)
	get lists of strings corresponding to a given property type More...
template<class TVariation >
static void	GetDeltas (list< string > &Alleles, const TVariation *pVariation)
	add alleles to a list of strings from deltas in variation data More...

Static Public Attributes
static const string	sResourceLink_RsID

Static Private Member Functions
template<class TPVariation >
static bool	x_CommonConvertFeat (TPVariation pVariation, const CSeq_feat &SrcFeat)

Detailed Description

set of functions for dealing with SNP represented as variation objects

Definition at line 249 of file snp_utils.hpp.

Member Enumeration Documentation

ESNPPropTypes

enum NSNPVariationHelper::ESNPPropTypes

enums to control getting a string list representation of various CVariantProperties

See also

VariantPropAsStrings

Enumerator
eSNPPropName_Undef
eSNPPropName_GeneLocation	prop.gene-location
eSNPPropName_Effect	prop.effect
eSNPPropName_Mapping	prop.mapping
eSNPPropName_FreqValidation	prop.frequence-based-validation
eSNPPropName_QualityCheck	prop.quality-check
eSNPPropName_ResourceLink	prop.resource-link
eSNPPropName_ResourceLinkURL	generate URL templates, with one of sResourceLink_ substrings potentially inside the user should perform correct substitution of sResourceLink_ substring for the actual value an empty string will be inserted into the list when the resource URL is not known the order is guaranteed to be exactly the same as for _ResourceLink for the same prop prop.resource-link

Definition at line 285 of file snp_utils.hpp.

Member Function Documentation

ConvertFeat() [1/2]

bool NSNPVariationHelper::ConvertFeat ( CVariation &  Variation, const CSeq_feat &  SrcFeat  )

static

legacy SNP feature conversion into a variation object

reads a feature that supposedly contains a SNP record (old, up-to-2012, style, with SNP data encoded as "qual" (alleles) and "ext.data" (bitfield)) and sets Variation to content found in the feature

Parameters

Variation	conversion result will be put here, old contents are destroyed upon conversion success
SrcFeat	old format feature

Returns

false if a given feature is not a correctly formed SNP feature

Definition at line 336 of file snp_utils.cpp.

References NSnp::GetBitfield(), CSeq_feat_Base::GetLocation(), CSnpBitfield::isGood(), MSerial_AsnText, CUser_object_Base::SetClass(), CUser_field_Base::SetData(), CVariation_Base::SetExt(), CUser_object::SetField(), CVariantPlacement_Base::SetLoc(), CVariation_Base::SetPlacements(), SNP_VAR_EXT_BITFIELD, SNP_VAR_EXT_CLASS, and x_CommonConvertFeat().

Referenced by CTestBMApp::Run().

ConvertFeat() [2/2]

bool NSNPVariationHelper::ConvertFeat ( CVariation_ref &  Variation, const CSeq_feat &  SrcFeat  )

static

See also

same as the other ConvertFeat(), but result put into variation-ref, placement is lost

Definition at line 359 of file snp_utils.cpp.

References NSnp::GetBitfield(), CSnpBitfield::isGood(), MSerial_AsnText, CVariation_ref::SetExt(), SNP_VAR_EXT_BITFIELD, SNP_VAR_EXT_CLASS, and x_CommonConvertFeat().

DecodeBitfield()

void NSNPVariationHelper::DecodeBitfield ( CVariantProperties &  prop, const CSnpBitfield &  bf  )

static

convert SNP bitfield data to respective fields in CVariantProperties

Parameters

prop	The result will be put here
bf	Bitfield that will be decoded

Note

Not all of the bitfield bit currently have direct correspondencies within CVariantProperties so they will be lost during the conversion

Definition at line 379 of file snp_utils.cpp.

References CSnpBitfield::e5PctMinorAllele1Plus, CSnpBitfield::e5PctMinorAlleleAll, CSnpBitfield::eAcceptor, CSnpBitfield::eDonor, CVariantProperties_Base::eEffect_frameshift, CVariantProperties_Base::eEffect_missense, CVariantProperties_Base::eEffect_stop_gain, CVariantProperties_Base::eEffect_stop_loss, CVariantProperties_Base::eEffect_synonymous, CSnpBitfield::eFrameshift, CVariantProperties_Base::eFrequency_based_validation_above_5pct_1plus, CVariantProperties_Base::eFrequency_based_validation_above_5pct_all, CVariantProperties_Base::eFrequency_based_validation_is_mutation, CVariantProperties_Base::eFrequency_based_validation_validated, CVariantProperties_Base::eGene_location_acceptor, CVariantProperties_Base::eGene_location_donor, CVariantProperties_Base::eGene_location_in_gene, CVariantProperties_Base::eGene_location_intron, CVariantProperties_Base::eGene_location_near_gene_3, CVariantProperties_Base::eGene_location_near_gene_5, CVariantProperties_Base::eGene_location_utr_3, CVariantProperties_Base::eGene_location_utr_5, CVariantProperties_Base::eGenotype_has_genotypes, CVariantProperties_Base::eGenotype_in_haplotype_set, CSnpBitfield::eHasAssemblyConflict, CSnpBitfield::eHasGenotype, CSnpBitfield::eHasGenotypeConflict, CSnpBitfield::eHasLinkOut, CSnpBitfield::eHasMemberSsConflict, CSnpBitfield::eHasOtherSameSNP, CSnpBitfield::eHasProvisionalTPA, CSnpBitfield::eHasSnp3D, CSnpBitfield::eInGene, CSnpBitfield::eInGene3, CSnpBitfield::eInGene5, CSnpBitfield::eInGenotypeKit, CSnpBitfield::eInHaplotypeSet, CSnpBitfield::eIntron, CSnpBitfield::eInUTR3, CSnpBitfield::eInUTR5, CSnpBitfield::eIsAssemblySpecific, CSnpBitfield::eIsClinical, CSnpBitfield::eIsContigAlleleAbsent, CSnpBitfield::eIsMutation, CSnpBitfield::eIsPrecious, CSnpBitfield::eIsStrainSpecific, CSnpBitfield::eIsValidated, CSnpBitfield::eIsWithdrawn, CVariantProperties_Base::eMapping_has_assembly_conflict, CVariantProperties_Base::eMapping_has_other_snp, CVariantProperties_Base::eMapping_is_assembly_specific, CSnpBitfield::eMissense, CVariantProperties_Base::eQuality_check_contig_allele_missing, CVariantProperties_Base::eQuality_check_genotype_conflict, CVariantProperties_Base::eQuality_check_non_overlapping_alleles, CVariantProperties_Base::eQuality_check_strain_specific, CVariantProperties_Base::eQuality_check_withdrawn_by_submitter, CVariantProperties_Base::eResource_link_clinical, CVariantProperties_Base::eResource_link_genotypeKit, CVariantProperties_Base::eResource_link_has3D, CVariantProperties_Base::eResource_link_preserved, CVariantProperties_Base::eResource_link_provisional, CVariantProperties_Base::eResource_link_submitterLinkout, CSnpBitfield::eStopGain, CSnpBitfield::eStopLoss, CSnpBitfield::eSynonymous, CSnpBitfield::GetVersion(), CSnpBitfield::IsTrue(), CVariantProperties_Base::SetEffect(), CVariantProperties_Base::SetFrequency_based_validation(), CVariantProperties_Base::SetGene_location(), CVariantProperties_Base::SetGenotype(), CVariantProperties_Base::SetMapping(), CVariantProperties_Base::SetQuality_check(), CVariantProperties_Base::SetResource_link(), and CVariantProperties_Base::SetVersion().

Referenced by x_CommonConvertFeat().

GetDeltas()

template<class TVariation >

void NSNPVariationHelper::GetDeltas ( list< string > &  Alleles, const TVariation *  pVariation  )

inlinestatic

add alleles to a list of strings from deltas in variation data

empty deltas are converted to dashes "-"

Parameters

Alleles	list of strings to the end of which the found deltas will be added, alleles already present in the list are retained
pVariation	variation object from which the deltas are read

Definition at line 329 of file snp_utils.hpp.

References CSeq_literal_Base::CanGetSeq_data(), CDelta_item_Base::C_Seq::e_Literal, CDelta_item_Base::C_Seq::e_This, CAliasBase< TPrim >::Get(), CSeq_data_Base::GetIupacaa(), CSeq_data_Base::GetIupacna(), CDelta_item_Base::C_Seq::GetLiteral(), CSeq_literal_Base::GetSeq_data(), CSeq_data_Base::IsIupacaa(), CSeq_data_Base::IsIupacna(), ITERATE, and CDelta_item_Base::C_Seq::Which().

VariantPropAsStrings()

void NSNPVariationHelper::VariantPropAsStrings ( list< string > &  ResList, const CVariantProperties &  prop, ESNPPropTypes  ePropType  )

static

get lists of strings corresponding to a given property type

Parameters

ResList	will be reset to the resulting list of strings
prop	property based upon values within which the result will be generated
ePropType	type of property requested

See also

ESNPPropTypes

Definition at line 536 of file snp_utils.cpp.

References CVariantProperties_Base::CanGetEffect(), CVariantProperties_Base::CanGetFrequency_based_validation(), CVariantProperties_Base::CanGetGene_location(), CVariantProperties_Base::CanGetMapping(), CVariantProperties_Base::CanGetQuality_check(), CVariantProperties_Base::CanGetResource_link(), CVariantProperties_Base::eEffect_down_regulator, CVariantProperties_Base::eEffect_frameshift, CVariantProperties_Base::eEffect_methylation, CVariantProperties_Base::eEffect_missense, CVariantProperties_Base::eEffect_no_change, CVariantProperties_Base::eEffect_nonsense, CVariantProperties_Base::eEffect_stop_gain, CVariantProperties_Base::eEffect_stop_loss, CVariantProperties_Base::eEffect_synonymous, CVariantProperties_Base::eEffect_up_regulator, CVariantProperties_Base::eFrequency_based_validation_above_1pct_1plus, CVariantProperties_Base::eFrequency_based_validation_above_1pct_all, CVariantProperties_Base::eFrequency_based_validation_above_5pct_1plus, CVariantProperties_Base::eFrequency_based_validation_above_5pct_all, CVariantProperties_Base::eFrequency_based_validation_is_mutation, CVariantProperties_Base::eFrequency_based_validation_validated, CVariantProperties_Base::eGene_location_acceptor, CVariantProperties_Base::eGene_location_conserved_noncoding, CVariantProperties_Base::eGene_location_donor, CVariantProperties_Base::eGene_location_in_gene, CVariantProperties_Base::eGene_location_in_start_codon, CVariantProperties_Base::eGene_location_in_stop_codon, CVariantProperties_Base::eGene_location_intergenic, CVariantProperties_Base::eGene_location_intron, CVariantProperties_Base::eGene_location_near_gene_3, CVariantProperties_Base::eGene_location_near_gene_5, CVariantProperties_Base::eGene_location_utr_3, CVariantProperties_Base::eGene_location_utr_5, CVariantProperties_Base::eMapping_has_assembly_conflict, CVariantProperties_Base::eMapping_has_other_snp, CVariantProperties_Base::eMapping_is_assembly_specific, CVariantProperties_Base::eQuality_check_contig_allele_missing, CVariantProperties_Base::eQuality_check_genotype_conflict, CVariantProperties_Base::eQuality_check_non_overlapping_alleles, CVariantProperties_Base::eQuality_check_strain_specific, CVariantProperties_Base::eQuality_check_withdrawn_by_submitter, CVariantProperties_Base::eResource_link_clinical, CVariantProperties_Base::eResource_link_genotypeKit, CVariantProperties_Base::eResource_link_has3D, CVariantProperties_Base::eResource_link_preserved, CVariantProperties_Base::eResource_link_provisional, CVariantProperties_Base::eResource_link_submitterLinkout, eSNPPropName_Effect, eSNPPropName_FreqValidation, eSNPPropName_GeneLocation, eSNPPropName_Mapping, eSNPPropName_QualityCheck, eSNPPropName_ResourceLink, eSNPPropName_ResourceLinkURL, CVariantProperties_Base::GetEffect(), CVariantProperties_Base::GetFrequency_based_validation(), CVariantProperties_Base::GetGene_location(), CVariantProperties_Base::GetMapping(), CVariantProperties_Base::GetQuality_check(), and CVariantProperties_Base::GetResource_link().

x_CommonConvertFeat()

template<class TPVariation >

bool NSNPVariationHelper::x_CommonConvertFeat ( TPVariation  pVariation, const CSeq_feat &  SrcFeat  )

inlinestaticprivate

Definition at line 379 of file snp_utils.hpp.

References DecodeBitfield(), CSnpBitfield::eDips, CSnpBitfield::eMicrosatellite, CSnpBitfield::eMultiBase, CVariation_ref::eSeqType_na, CSnpBitfield::eSingleBase, CVariation_inst_Base::eType_other, NSnp::GetAlleles(), NSnp::GetBitfield(), CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), NSnp::GetRsid(), NSnp::GetTag(), CSnpBitfield::GetVariationClass(), CSnpBitfield::isGood(), CVariation_ref_Base::C_Data::IsInstance(), NSnp::IsSnp(), NStr::Join(), CVariation_ref_Base::SetData(), CVariation_ref::SetDeletionInsertion(), CVariation_ref::SetMNP(), and CVariation_ref::SetSNV().

Referenced by ConvertFeat().

Member Data Documentation

sResourceLink_RsID

const string NSNPVariationHelper::sResourceLink_RsID

static

Definition at line 281 of file snp_utils.hpp.

---

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

• include/objtools/snputil/snp_utils.hpp
• src/objtools/snputil/snp_utils.cpp