From 10def1e26c74e54c95b5f34dce4b861250e515bf Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Tue, 18 Jul 2023 09:25:46 -0400
Subject: [PATCH] fix merge add cell id bug

---
 R/Utilities.R | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/R/Utilities.R b/R/Utilities.R
index 08c8a509f..45928ee70 100644
--- a/R/Utilities.R
+++ b/R/Utilities.R
@@ -867,8 +867,32 @@ Merge_Seurat_List <- function(
     }
   }
 
+  # Check all barcodes are unique to begin with
+  duplicated_barcodes <- list_seurat %>%
+    lapply(colnames) %>%
+    unlist() %>%
+    duplicated() %>%
+    any()
+
+  if (duplicated_barcodes && is.null(x = add_cell_ids)) {
+    cli_abort(message = c("There are overlapping cell barcodes present in the input objects",
+                          "i" = "Please rename cells or provide prefixes to {.code add.cell.ids} parameter to make unique.")
+    )
+  }
+
+  # Check right number of suffix/prefix ids are provided
+  if (!is.null(x = add_cell_ids) && length(x = add_cell_ids) != length(x = list_seurat)) {
+    cli_abort(message = "The number of prefixes in {.code add.cell.ids} must be equal to the number of objects supplied to {.code list_seurat}.")
+  }
+
+  # Rename cells if provided
+  list_seurat <- lapply(1:length(list_seurat), function(x) {
+    list_seurat[[x]] <- RenameCells(object = list_seurat[[x]], add.cell.id = add.cell.ids[x])
+  })
+
+  # Merge objects
   merged_object <- reduce(list_seurat, function(x, y) {
-    merge(x = x, y = y, add.cell.ids = add.cell.ids, merge.data = merge.data, project = project)
+    merge(x = x, y = y, merge.data = merge.data, project = project)
   })
 }