hotfix-4.5.x: bugfix. variant-annotation CLI now correctly passes the assembly argument when annotating through WS
@@ -815,6 +815,8 @@ public class VariantAnnotationCommandExecutor extends CommandExecutor {
// Assembly
if (variantAnnotationCommandOptions.assembly != null) {
assembly = variantAnnotationCommandOptions.assembly;
+ // In case annotation is made through WS assembly must be set in the queryOptions
+ queryOptions.put("assembly", variantAnnotationCommandOptions.assembly);
} else {
assembly = null;
logger.warn("No assembly provided. Using default assembly for {}", species);
