# HG changeset patch
# User devteam
# Date 1393278969 18000
# Node ID 55b6cd128a410bbc3390c5eaa593da0f54b97140
# Parent  6ad4014eddd73e09948c26bb6ce0360147bf9e54
Uploaded

diff -r 6ad4014eddd7 -r 55b6cd128a41 fastq2sam_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq2sam_wrapper.sh	Mon Feb 24 16:56:09 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