update mummer_alignment to print message when error

Author: nvelden

R/cluster_blast.R

@@ -68,7 +68,6 @@ get_protein_combinations <- function(data, cluster_pair, rowIDs = NULL) {
 #' patterns <- c("ACDEFGHIKLMNPQRSTVWY", "ACDGFHIKLMNPQRSTVWY")
 #' subjects <- c("ACDEFGHIKLMNPQRSTVWY", "TCDGFHIKLMNPQRSTVWY")
 #' result <- compute_identity(patterns, subjects)
-#' print(result)
 #'
 #' @noRd
 compute_identity <- function(patterns, subjects) {

R/mummer_alignment.R

@@ -173,7 +173,8 @@ mummer_alignment <- function(
       return(coords)
 
     }, error = function(e) {
-      cat(sprintf("Error in aligning %s vs %s: %s\n", pair[1], pair[2], e$message))
+      warning(sprintf("Error in aligning %s vs %s: %s", pair[1], pair[2], e$message))
+      return(NULL)
     })
   })