# HG changeset patch
# User devteam
# Date 1393300606 18000
# Node ID 7d0d25eabacb3d05a26c9e840a9b366c1077a36b
# Parent  bd86ab3d004c15ed356fa60e08f815eb48ad92ed
Uploaded

diff -r bd86ab3d004c -r 7d0d25eabacb fastq2sam_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq2sam_wrapper.sh	Mon Feb 24 22:56:46 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} 2>&1
+
+if [ "$1" == "sam" ]
+then
+    mv $2.sam $2
+fi