// ----------------------------------------------------------------------------
bool
CVcfReader::xProcessDataLine(
const string& line,
CRef<CSeq_annot> pAnnot,
IMessageListener* pEC)
// ----------------------------------------------------------------------------
{
if ( NStr::StartsWith( line, "#" ) ) {
return false;
}
CVcfData data;
if (!xParseData(line, data, pEC)) {
return false;
}
CRef<CSeq_feat> pFeat( new CSeq_feat );
pFeat->SetData().SetVariation().SetData().SetSet().SetType(
CVariation_ref::C_Data::C_Set::eData_set_type_package );
pFeat->SetData().SetVariation().SetVariant_prop().SetVersion( 5 );
CSeq_feat::TExt& ext = pFeat->SetExt();
ext.SetType().SetStr( "VcfAttributes" );
if (!xAssignFeatureLocationSet(data, pFeat)) {
return false;
}
if (!xAssignVariationIds(data, pFeat)) {
return false;
}
if (!xAssignVariationAlleleSet(data, pFeat)) {
return false;
}
if (!xProcessScore(data, pFeat)) {
return false;
}
if (!xProcessFilter(data, pFeat)) {
return false;
}
if (!xProcessInfo( data, pFeat, pEC)) {
return false;
}
if (!xProcessFormat(data, pFeat)) {
return false;
}
if ( pFeat->GetExt().GetData().empty() ) {
pFeat->ResetExt();
}
pAnnot->SetData().SetFtable().push_back( pFeat );
return true;
}
// ----------------------------------------------------------------------------
bool
CVcfReader::xProcessVariant(
const CVcfData& data,
unsigned int index,
CRef<CSeq_annot> pAnnot)
// ----------------------------------------------------------------------------
{
CRef<CSeq_feat> pFeat( new CSeq_feat );
pFeat->SetData().SetVariation().SetData().SetSet().SetType(
CVariation_ref::C_Data::C_Set::eData_set_type_package );
pFeat->SetData().SetVariation().SetVariant_prop().SetVersion( 5 );
CSeq_feat::TExt& ext = pFeat->SetExt();
ext.SetType().SetStr( "VcfAttributes" );
if ( ! xAssignFeatureLocation( data, index, pFeat ) ) {
return false;
}
if ( ! x_AssignVariationIds( data, pFeat ) ) {
return false;
}
if ( ! xAssignVariationAlleles( data, index, pFeat ) ) {
return false;
}
if ( ! x_ProcessScore( data, pFeat ) ) {
return false;
}
if ( ! x_ProcessFilter( data, pFeat ) ) {
return false;
}
if ( ! x_ProcessInfo( data, pFeat ) ) {
return false;
}
if ( ! x_ProcessFormat( data, pFeat ) ) {
return false;
}
if ( pFeat->GetExt().GetData().empty() ) {
pFeat->ResetExt();
}
pAnnot->SetData().SetFtable().push_back( pFeat );
return true;
}