From 59875ea56512ed10443aa17420bb7e007b579281 Mon Sep 17 00:00:00 2001
From: Li <mourisl@hotmail.com>
Date: Tue, 27 Jul 2021 12:41:01 -0400
Subject: [PATCH] Fix a serious bug in wrapper for not generating cdr3 report
 file when input barcode file

---
 run-trust4 | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/run-trust4 b/run-trust4
index 26971f2..2a02cc3 100755
--- a/run-trust4
+++ b/run-trust4
@@ -400,6 +400,10 @@ if ( $stage <= 2 )
 	{
 		$annotatorArgs .= " -r ${prefix}_assembled_reads.fa" ;
 	}
+	else
+	{
+		$annotatorArgs .= " --outputCDR3File" ;
+	}
 
 	if ( $vdjcRef eq "" )
 	{