start fixing for cell ranger 9 changes

samuel-marsh · Dec 3, 2024 · 6e01614 · 6e01614
1 parent 1ec9850
commit 6e01614
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/R/Read_&_Write_Data.R b/R/Read_&_Write_Data.R
@@ -1575,7 +1575,12 @@ Read_Metrics_10X <- function(
   # Check if single file
   file_ending <- grep(pattern = ".csv$", x = base_path, value = TRUE)
   if (length(x = file_ending) == 1) {
-    metrics_data <- Metrics_Single_File(base_path = base_path, cellranger_multi = cellranger_multi)
+    temp_csv <- read.csv(file = base_path)
+    if (ncol(x = temp_csv) > nrow(x = temp_csv)) {
+      metrics_data <- Metrics_Single_File(base_path = base_path, cellranger_multi = cellranger_multi)
+    } else {
+      metrics_data <- Metrics_Single_File_v9plus(base_path = base_path, cellranger_multi = cellranger_multi)
+    }
     return(metrics_data)
   }