# HG changeset patch
# User devteam
# Date 1393372541 18000
# Node ID a85055d2093713e0ad03d736d90f697daa4e3d85
# Parent  21bf2afb895ca428d0f996307cf93d1dfc87fe4a
Uploaded

diff -r 21bf2afb895c -r a85055d20937 mergebamalignment_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergebamalignment_wrapper.sh	Tue Feb 25 18:55:41 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