update import_vdj error messages

rnabioco · Oct 8, 2023 · 4358cbd · 4358cbd
1 parent 97d9c2d
commit 4358cbd
Showing 1 changed file with 16 additions and 17 deletions.
diff --git a/R/import-vdj.R b/R/import-vdj.R
@@ -169,9 +169,9 @@ import_vdj <- function(input = NULL, vdj_dir = NULL, prefix = "",
     filter_chains <- TRUE
 
     cli::cli_warn(
-      "When `include_mutations` is `TRUE`, `filter_chains` is also
+      "When `include_mutations` is `TRUE`, `filter_chains` is
        automatically set `TRUE` since mutation data is only available for
-       productive chains."
+       productive chains"
     )
   }
 
@@ -193,7 +193,6 @@ import_vdj <- function(input = NULL, vdj_dir = NULL, prefix = "",
   len_cols   <- paste0(seq_cols, "_length")
 
   # Columns containing per-cell info
-  # cell_cols <- c("barcode", "clonotype_id")
   cell_cols <- c("barcode", "clonotype_id", "paired")
 
   # Optional aggr columns
@@ -319,24 +318,23 @@ import_vdj <- function(input = NULL, vdj_dir = NULL, prefix = "",
       indel_cols <- indel_cols[indel_cols != "contig_id"]
 
       # Join indel data
-      # SHOULD CHECK BARCODE OVERLAP HERE!!!
-      # IF BARCODES DO NOT OVERLAP HERE, WILL RETURN ALL 0s
+      # check that barcodes match
+      # if barcodes do not match, 0s will get added for mutation columns
       indel_ctigs <- purrr::map2(
         contigs, indels, dplyr::left_join, by = "contig_id",
         relationship = "many-to-one"
       )
 
       purrr::walk2(contigs, indels, ~ {
-        indel_ovlp <- sum(.y$contig_id %in% .x$contig_id) / nrow(.y)
-
-        if (indel_ovlp < 1) {
-          cli::cli_abort(
-            "Barcodes from mutation data do not match, check your input files."
+        if (any(!.y$contig_id %in% .x$contig_id)) {
+          .malformed_data_error(
+            "cell barcodes from concat_ref.bam and
+             filtered_contig_annotations.csv do not match"
           )
         }
       })
 
-      # Replace NAs with 0
+      # Replace NAs with 0s
       # contigs that did not have any mutations will have NAs
       indel_ctigs <- purrr::map(
         indel_ctigs,
@@ -541,9 +539,7 @@ import_vdj <- function(input = NULL, vdj_dir = NULL, prefix = "",
     .data$clonotype_id != "None", !is.na(.data$clonotype_id)
   )
 
-  if (nrow(res) == 0) {
-    .malformed_data_error("no valid clonotypes present")
-  }
+  if (nrow(res) == 0) .malformed_data_error("no valid clonotypes present")
 
   # Add prefix to V(D)J columns
   res <- dplyr::rename_with(res, ~ paste0(prefix, .x))
@@ -936,7 +932,9 @@ import_vdj <- function(input = NULL, vdj_dir = NULL, prefix = "",
   )
 
   if (ncol(res) == 1) {
-    cli::cli_abort("V(D)J coordinates not found, check {.file airr_file}")
+    msg <- "columns containing V(D)J coordinates were not found in "
+
+    .malformed_data_error(paste0(msg, basename(airr_file)))
   }
 
   res <- tidyr::pivot_longer(res, -"contig_id")
@@ -1469,13 +1467,14 @@ import_vdj <- function(input = NULL, vdj_dir = NULL, prefix = "",
 #' Malformed data error
 #'
 #' @noRd
-.malformed_data_error <- function(msg) {
+.malformed_data_error <- function(msg, call = NULL) {
   cli::cli_abort(
     "Malformed input data, {msg}. Did you modify the `cellranger` output
      files? {.fn import_vdj} requires files that are in the format generated by
      `cellranger`.
      If you are having trouble loading your data, please file an issue at
-     {.url https://github.com/rnabioco/djvdj/issues}."
+     {.url https://github.com/rnabioco/djvdj/issues}.",
+    call = call
   )
 }