--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split.sh	Tue Dec 18 09:20:12 2012 -0500
@@ -0,0 +1,25 @@
+#!bin/bash
+
+#purpose: shell script which performs the split option
+#author: Ziru Zhou
+#date: October, 2012
+
+main()
+{
+	output1="${1}"
+	output2="${2}"
+	input="${3}"
+
+	$(samtools view -H ${input} > tmp)
+	linecount=$(samtools view ${input} | wc -l)
+	half=$(((${linecount} + 1) / 2))
+	samtools view ${input} | shuf | split -d -l ${half}
+
+	$(cat tmp x00 > x00h)
+	$(cat tmp x01 > x01h)
+        samtools view -bSo ${output1} x00h
+        samtools view -bSo ${output2} x01h
+
+	rm tmp x00h x01h x00 x01
+}
+main "${@}"