Commit d38f34eb authored by sallet's avatar sallet
Browse files

allow to read tRNA and rRNA in reference annotation

parent f1be8460
......@@ -1304,7 +1304,6 @@ void Prediction::LoadGene(std::vector <GeneFeature*>& vGeneFeatures, std::vector
{
continue;
}
//cout << "voila : " << (*it)->getLocus()->getStart()<< "\n";
// E.Intr ou E.Term => Add an intron
if ( idSo=="SO:0000316" && (ontology_term=="SO:0000004" || ontology_term=="SO:0000197"))
......@@ -1379,7 +1378,7 @@ void Prediction::LoadGene(std::vector <GeneFeature*>& vGeneFeatures, std::vector
vPos.push_back ( end );
vState.push_back( IntrF1+k );
}
else if (idSo=="SO:0000655") { // ncRNA
else if (idSo=="SO:0000655" || idSo=="SO:0000253" || idSo=="SO:0000252") { // ncRNA/tRNA or rRNA
vPos.push_back ( end );
vState.push_back( RnaF );
}
......@@ -1420,7 +1419,7 @@ void Prediction::LoadGene(std::vector <GeneFeature*>& vGeneFeatures, std::vector
idSo=tmp;
}
if ( idSo!="SO:0000316" && idSo!="SO:0000204" && idSo!="SO:0000205" && idSo !="SO:0000655")
if ( idSo!="SO:0000316" && idSo!="SO:0000204" && idSo!="SO:0000205" && idSo !="SO:0000655" && idSo != "SO:0000253" && idSo != "SO:0000252")
{
continue;
}
......@@ -1506,7 +1505,7 @@ void Prediction::LoadGene(std::vector <GeneFeature*>& vGeneFeatures, std::vector
vtmpState.push_back( IntrR1+k );
intron_end_pos = start-1; // to add an intron on next step
}
else if (idSo=="SO:0000655") { // ncRNA
else if (idSo=="SO:0000655" || idSo=="SO:0000253" || idSo=="SO:0000252") { // ncRNA or tRNA or rRNA
vtmpPos.push_back ( end );
vtmpState.push_back( RnaR );
}
......
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