// ----------------------------------------------------------------------------
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::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;
}
