From 4b2e0039b564e43ff37f5107383105cf48e576cd Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sat, 25 Jul 2020 16:07:23 -0500
Subject: [PATCH] update warning in perl -i
---
variants/svcalling.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index 28812c1..be79e49 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -64,7 +64,7 @@ mkdir -p temp
if [[ -z $tid ]]
then
- tid=`samtools view -H ${sbam} |grep '^@RG' |perl -pi -e 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
+ tid=`samtools view -H ${sbam} |grep '^@RG' |perl -pe 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
fi
bams=''
--
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