# HG changeset patch
# User devteam
# Date 1393392777 18000
# Node ID 4f83d10e21792caf508e34860369e9364ddf059c
# Parent  0c7d738f5c44be33b388d7b1e8b676628ca6a23d
Uploaded

diff -r 0c7d738f5c44 -r 4f83d10e2179 mergebamalignment_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergebamalignment_wrapper.sh	Wed Feb 26 00:32:57 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