Removed reindexing of feature files, when they are added as annotations to reference genome. Maybe useful for large VCF files.
@@ -45,7 +45,6 @@ import com.epam.catgenome.entity.BiologicalDataItemResourceType;
import com.epam.catgenome.entity.FeatureFile;
import com.epam.catgenome.entity.gene.GeneFile;
import com.epam.catgenome.exception.FeatureIndexException;
-import com.epam.catgenome.manager.FeatureIndexManager;
import com.epam.catgenome.util.AuthUtils;
import com.epam.catgenome.util.ListMapCollector;
import org.apache.commons.collections4.CollectionUtils;
@@ -89,9 +88,6 @@ public class ReferenceGenomeManager {
@Autowired
private SpeciesDao speciesDao;
- @Autowired
- private FeatureIndexManager featureIndexManager;
-
private static final Set<BiologicalDataItemFormat> ANNOTATION_FORMATS = new HashSet<>();
static {
ANNOTATION_FORMATS.add(BiologicalDataItemFormat.BED);
@@ -401,7 +397,6 @@ public class ReferenceGenomeManager {
loadReferenceGenome(referenceId).getName()
)
);
- featureIndexManager.buildIndexForFile(annotationFile);
referenceGenomeDao.addAnnotationFile(referenceId, annotationFileBiologicalItemId);
}
return loadReferenceGenome(referenceId);
