@@ -151,13 +151,19 @@ calculateMappingBiasGatk4 <- function(workspace, reference.genome,

         .stopUserError("Install the genomicsdb and jsonlite R packages for GenomicsDB import.")

     }

     workspace <- normalizePath(workspace, mustWork = TRUE)

-

-    db <- genomicsdb::connect(workspace = workspace,

-        vid_mapping_file = file.path(workspace, "vidmap.json"),

-        callset_mapping_file = file.path(workspace, "callset.json"),

-        reference_genome = reference.genome,

-        c("DP", "AD", AF.info.field))

-

+    

+    if (!is.null(formals(genomicsdb::connect)$reference_genome)) {

+        db <- genomicsdb::connect(workspace = workspace,

+            vid_mapping_file = file.path(workspace, "vidmap.json"),

+            callset_mapping_file = file.path(workspace, "callset.json"),

+            reference_genome = reference.genome,

+            attributes = c("DP", "AD", AF.info.field))

+    } else {

+        db <- genomicsdb::connect(workspace = workspace,

+            vid_mapping_file = file.path(workspace, "vidmap.json"),

+            callset_mapping_file = file.path(workspace, "callset.json"),

+            attributes = c("DP", "AD", AF.info.field))

+    }    

     jcallset <- jsonlite::read_json(file.path(workspace, "callset.json"))

     jvidmap <- jsonlite::read_json(file.path(workspace, "vidmap.json"))