From ce41f5443c73a32ae185dfb943e3cdf0dc61f8c1 Mon Sep 17 00:00:00 2001
From: Andrew Thrasher <adthrasher@gmail.com>
Date: Mon, 28 Jun 2021 11:59:32 -0400
Subject: [PATCH] Add missing script to DNAnexus app folder

---
 dx_app/resources/stjude/bin/getReadLength.sh | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100755 dx_app/resources/stjude/bin/getReadLength.sh

diff --git a/dx_app/resources/stjude/bin/getReadLength.sh b/dx_app/resources/stjude/bin/getReadLength.sh
new file mode 100755
index 0000000..1804f21
--- /dev/null
+++ b/dx_app/resources/stjude/bin/getReadLength.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+bamfile=$1
+
+samtools view $bamfile | head -n 1000 | cut -f 10 | awk '{ print length($0) }' | sort -n | tail -n 1