From 5aba18896929d6d4fcd06a8a9babf66cf33a0092 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 20 Dec 2014 22:27:27 -0500
Subject: [PATCH] write empty .gt file as a placeholder

to suppress error messages from run-bwamem
---
 bwakit/typeHLA.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bwakit/typeHLA.sh b/bwakit/typeHLA.sh
index b5a2b4e..b73100d 100755
--- a/bwakit/typeHLA.sh
+++ b/bwakit/typeHLA.sh
@@ -15,6 +15,7 @@ fi
 preres="resource-human-HLA"
 root=`dirname $0`
 pre=$1.$2
+touch $pre.gt
 
 if [ ! -s $pre.fq ]; then
 	echo '** Empty input file. Abort!' >&2