// ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantIns(
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]);
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->SetAction(CDelta_item::eAction_ins_before);
pItem->SetSeq().SetLiteral(*pLiteral);
CVariation_inst& instance = pVariant->SetData().SetInstance();
instance.SetType(CVariation_inst::eType_ins);
instance.SetDelta().push_back(pItem);
}}
variants.push_back(pVariant);
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]);
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();
//Let's try to smartly set the Type.
if( data.m_Alt[index].size() == 1 && data.m_strRef.size() == 1) {
instance.SetType(CVariation_inst::eType_snv);
} else {
instance.SetType(CVariation_inst::eType_delins);
}
instance.SetDelta().push_back(pItem);
}}
variants.push_back(pVariant);
return true;
}
// ----------------------------------------------------------------------------
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::xAssignVariationAlleles(
const CVcfData& data,
unsigned int index,
CRef<CSeq_feat> pFeature )
// ----------------------------------------------------------------------------
{
if (data.IsSnv(index)) {
return xAssignVariantSnv(data, index, pFeature);
}
if (data.IsDel(index)) {
return xAssignVariantDel(data, index, pFeature);
}
if (data.IsIns(index)) {
return xAssignVariantIns(data, index, pFeature);
}
if (data.IsDelins(index)) {
return xAssignVariantDelins(data, index, pFeature);
}
CVariation_ref::TData::TSet::TVariations& variants =
pFeature->SetData().SetVariation().SetData().SetSet().SetVariations();
CRef<CVariation_ref> pVariant(new CVariation_ref);
string note("Warning: Could not place variation for record \"" +
NStr::Replace(data.m_strLine.substr(0, 40), "\t", " "));
if (data.m_strLine.size() > 40) {
note += "...";
}
note += "\". Offending values: ref=\"" + data.m_strRef +
"\", alt=\"" + data.m_Alt[index] + "\"";
pVariant->SetData().SetNote(note);
variants.push_back(pVariant);
return true;
}
// ----------------------------------------------------------------------------
bool
CVcfReader::xAssignVariantMnv(
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->SetMNP(variant, CVariation_ref::eSeqType_na);
}}
variants.push_back(pVariant);
return true;
}
// ----------------------------------------------------------------------------
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);
return true;
}