// ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantDel(
const CVcfData& data,
unsigned int index,
CRef<CSeq_feat> pFeature )
// ----------------------------------------------------------------------------
{
CVariation_ref::TData::TSet::TVariations& variants =
pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();
CRef<CVariation_ref> pVariant(new CVariation_ref);
{{
//pVariant->SetData().SetNote("DEL");
pVariant->SetDeletion();
CVariation_inst& instance = pVariant->SetData().SetInstance();
CRef<CDelta_item> pItem(new CDelta_item);
pItem->SetAction(CDelta_item::eAction_del_at);
pItem->SetSeq().SetThis();
instance.SetDelta().push_back(pItem);
}}
variants.push_back(pVariant);
CRef<CVariation_ref> pIdentity(new CVariation_ref);
{{
//pIdentity->SetData().SetNote("IDENTITY");
vector<string> variant;
variant.push_back(data.m_strRef);
pIdentity->SetSNV(variant, CVariation_ref::eSeqType_na);
CVariation_inst& instance = pIdentity->SetData().SetInstance();
instance.SetType(CVariation_inst::eType_identity);
instance.SetObservation(CVariation_inst::eObservation_asserted);
}}
variants.push_back(pIdentity);
return true;
}
// ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantSnv(
const CVcfData& data,
unsigned int index,
CRef<CSeq_feat> pFeature )
// ----------------------------------------------------------------------------
{
CVariation_ref::TData::TSet::TVariations& variants =
pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();
CRef<CVariation_ref> pVariant(new CVariation_ref);
{{
vector<string> variant;
variant.push_back(data.m_Alt[index]);
pVariant->SetSNV(variant, CVariation_ref::eSeqType_na);
}}
variants.push_back(pVariant);
CRef<CVariation_ref> pIdentity(new CVariation_ref);
{{
vector<string> variant;
variant.push_back(data.m_strRef);
pIdentity->SetSNV(variant, CVariation_ref::eSeqType_na);
CVariation_inst& instance = pIdentity->SetData().SetInstance();
instance.SetType(CVariation_inst::eType_identity);
instance.SetObservation(CVariation_inst::eObservation_asserted);
}}
variants.push_back(pIdentity);
return true;
}
// ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantDelins(
const CVcfData& data,
unsigned int index,
CRef<CSeq_feat> pFeature )
// ----------------------------------------------------------------------------
{
CVariation_ref::TData::TSet::TVariations& variants =
pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();
CRef<CVariation_ref> pVariant(new CVariation_ref);
{{
string insertion(data.m_Alt[index].substr(1));
CRef<CSeq_literal> pLiteral(new CSeq_literal);
pLiteral->SetSeq_data().SetIupacna().Set(insertion);
pLiteral->SetLength(insertion.size());
CRef<CDelta_item> pItem(new CDelta_item);
pItem->SetSeq().SetLiteral(*pLiteral);
CVariation_inst& instance = pVariant->SetData().SetInstance();
instance.SetType(CVariation_inst::eType_mnp);
instance.SetDelta().push_back(pItem);
}}
variants.push_back(pVariant);
CRef<CVariation_ref> pIdentity(new CVariation_ref);
{{
string insertion(data.m_strRef.substr(1));
CRef<CSeq_literal> pLiteral(new CSeq_literal);
pLiteral->SetSeq_data().SetIupacna().Set(insertion);
pLiteral->SetLength(insertion.size());
CRef<CDelta_item> pItem(new CDelta_item);
pItem->SetSeq().SetLiteral(*pLiteral);
CVariation_inst& instance = pIdentity->SetData().SetInstance();
instance.SetType(CVariation_inst::eType_identity);
instance.SetDelta().push_back(pItem);
instance.SetObservation(CVariation_inst::eObservation_asserted);
}}
variants.push_back(pIdentity);
return true;
}
// ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariationAlleleSet(
const CVcfData& data,
CRef<CSeq_feat> pFeature )
// ----------------------------------------------------------------------------
{
CVariation_ref::TData::TSet::TVariations& variants =
pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();
//make one variation for the reference
CRef<CVariation_ref> pIdentity(new CVariation_ref);
vector<string> variant;
switch(data.m_SetType) {
case CVcfData::ST_ALL_INS:
pIdentity->SetDeletion();
break;
default:
variant.push_back(data.m_strRef);
pIdentity->SetSNV(variant, CVariation_ref::eSeqType_na);
break;
}
CVariation_inst& instance = pIdentity->SetData().SetInstance();
instance.SetType(CVariation_inst::eType_identity);
instance.SetObservation(CVariation_inst::eObservation_reference);
if (data.m_SetType != CVcfData::ST_ALL_INS) {
variants.push_back(pIdentity);
}
//add additional variations, one for each alternative
for (unsigned int i=0; i < data.m_Alt.size(); ++i) {
switch(data.m_SetType) {
default:
if (!xAssignVariantDelins(data, i, pFeature)) {
return false;
}
break;
case CVcfData::ST_ALL_SNV:
if (!xAssignVariantSnv(data, i, pFeature)) {
return false;
}
break;
case CVcfData::ST_ALL_MNV:
if (!xAssignVariantMnv(data, i, pFeature)) {
return false;
}
break;
case CVcfData::ST_ALL_INS:
if (!xAssignVariantIns(data, i, pFeature)) {
return false;
}
break;
case CVcfData::ST_ALL_DEL:
if (!xAssignVariantDel(data, i, pFeature)) {
return false;
}
break;
}
}
return true;
}
