# HG changeset patch
# User devteam
# Date 1391304026 18000
# Node ID 11e69ba20b85763e7d527fd2946f4004f10a50ec
# Parent  f7ebcc9dfb867489c245f8504f671e8a26ed0fa9
Uploaded

diff -r f7ebcc9dfb86 -r 11e69ba20b85 mergebamalignment_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergebamalignment_wrapper.sh	Sat Feb 01 20:20:26 2014 -0500
@@ -0,0 +1,5 @@
+#!/bin/bash
+reference_without_extension=${3%.*}
+java -jar $JAVA_JAR_PATH/CreateSequenceDictionary.jar R=$3 O=$reference_without_extension.dict
+eval java -Xmx2G -jar $JAVA_JAR_PATH/MergeBamAlignment.jar O=$1.$2 R=$3 ${*:4}
+mv $1.$2 $1