# HG changeset patch
# User devteam
# Date 1390523512 18000
# Node ID 86e7e072c4c9f402753b6e4cf3149bd5f0704cc5
# Parent  8b335563c71a097f177c6cf0cf87ddc847c8e62a
Uploaded

diff -r 8b335563c71a -r 86e7e072c4c9 fastq2sam_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq2sam_wrapper.sh	Thu Jan 23 19:31:52 2014 -0500
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+if [ "$1" == "sam" ]
+then
+    output=$2.sam
+else
+    output=$2
+fi
+
+java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "$JAVA_JAR_PATH/FastqToSam.jar" SAMPLE_NAME="$3" READ_GROUP_NAME="$4" OUTPUT=$output ${*:5}
+
+if [ "$1" == "sam" ]
+then
+    mv $2.sam $2
+fi