Choose the normal phenotype sequence for TRBJ2-2

src/alignment.r

@@ -34,7 +34,11 @@ parse_metadata <- function(metadata) {
 #' @return A \code{character} containing the gene sequence
 match_id_sequence <- function(names, vdj_segments, id) {
   matches <- grep(names, pattern = id)
+  if(id == "TRBJ2-2"){
+    row <- matches[2]
+  } else {
     row <- matches[1]
+  }
   return(as.character(vdj_segments[row]))
 }