From e4189cab013da6882998bc5e6eadc5a50966cd7a Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Sat, 15 May 2021 17:36:58 +0200
Subject: [PATCH] Choose the normal phenotype sequence for TRBJ2-2

---
 src/alignment.r | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/alignment.r b/src/alignment.r
index e213c4f..03470d3 100644
--- a/src/alignment.r
+++ b/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)
-  row <- matches[1]
+  if(id == "TRBJ2-2"){
+    row <- matches[2]
+  } else {
+    row <- matches[1]
+  }
   return(as.character(vdj_segments[row]))
 }